| Process Name | -Software | -Version | -
|---|---|---|
| {process if (i == 0) else ''} | -{tool} | -{version} | -
| Process Name | +Software | +Version | +
|---|---|---|
| {process if (i == 0) else ''} | +{tool} | +{version} | +
versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/learnreadorientationmodel/functions.nf b/modules/gatk4/learnreadorientationmodel/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/learnreadorientationmodel/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf
index b8aee764..5e9700e3 100644
--- a/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/modules/gatk4/learnreadorientationmodel/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_LEARNREADORIENTATIONMODEL {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(f1r2)
@@ -26,7 +15,8 @@ process GATK4_LEARNREADORIENTATIONMODEL {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def inputs_list = []
f1r2.each() { a -> inputs_list.add(" -I " + a) }
"""
@@ -34,11 +24,11 @@ process GATK4_LEARNREADORIENTATIONMODEL {
LearnReadOrientationModel \\
${inputs_list.join(' ')} \\
-O ${prefix}.tar.gz \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/markduplicates/functions.nf b/modules/gatk4/markduplicates/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/markduplicates/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf
index e44f4bfc..9f0b46da 100644
--- a/modules/gatk4/markduplicates/main.nf
+++ b/modules/gatk4/markduplicates/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_MARKDUPLICATES {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(bams)
@@ -28,7 +17,8 @@ process GATK4_MARKDUPLICATES {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def bam_list = bams.collect(){ bam -> "--INPUT ".concat(bam.toString()) }.join(" ")
def avail_mem = 3
if (!task.memory) {
@@ -43,11 +33,11 @@ process GATK4_MARKDUPLICATES {
--TMP_DIR . \\
--CREATE_INDEX true \\
--OUTPUT ${prefix}.bam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/mergebamalignment/functions.nf b/modules/gatk4/mergebamalignment/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/mergebamalignment/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf
index 9c5fe26c..01effb0f 100644
--- a/modules/gatk4/mergebamalignment/main.nf
+++ b/modules/gatk4/mergebamalignment/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_MERGEBAMALIGNMENT {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(aligned)
@@ -29,18 +18,19 @@ process GATK4_MERGEBAMALIGNMENT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
gatk MergeBamAlignment \\
ALIGNED=$aligned \\
UNMAPPED=$unmapped \\
R=$fasta \\
O=${prefix}.bam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/mergevcfs/functions.nf b/modules/gatk4/mergevcfs/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/mergevcfs/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf
index 28073fcb..cbfc2e9d 100644
--- a/modules/gatk4/mergevcfs/main.nf
+++ b/modules/gatk4/mergevcfs/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_MERGEVCFS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(vcfs)
@@ -28,7 +17,8 @@ process GATK4_MERGEVCFS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
// Make list of VCFs to merge
def input = ""
@@ -41,11 +31,11 @@ process GATK4_MERGEVCFS {
$input \\
O=${prefix}.vcf.gz \\
$ref \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/mutect2/functions.nf b/modules/gatk4/mutect2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/mutect2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index e0e2661b..662b3f0c 100644
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_MUTECT2 {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta) , path(input) , path(input_index) , val(which_norm)
@@ -40,7 +29,8 @@ process GATK4_MUTECT2 {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def panels_command = ''
def normals_command = ''
@@ -70,11 +60,11 @@ process GATK4_MUTECT2 {
${normals_command} \\
${panels_command} \\
-O ${prefix}.vcf.gz \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/revertsam/functions.nf b/modules/gatk4/revertsam/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/revertsam/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 7b5ee696..bca31a29 100644
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_REVERTSAM {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -26,16 +15,17 @@ process GATK4_REVERTSAM {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
gatk RevertSam \\
I=$bam \\
O=${prefix}.reverted.bam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/samtofastq/functions.nf b/modules/gatk4/samtofastq/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/samtofastq/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf
index 843c61ce..aa9a6b2d 100644
--- a/modules/gatk4/samtofastq/main.nf
+++ b/modules/gatk4/samtofastq/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_SAMTOFASTQ {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -26,17 +15,18 @@ process GATK4_SAMTOFASTQ {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
"""
gatk SamToFastq \\
I=$bam \\
$output \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/splitncigarreads/functions.nf b/modules/gatk4/splitncigarreads/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/splitncigarreads/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index 26fb799d..32d36df9 100644
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_SPLITNCIGARREADS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -29,17 +18,18 @@ process GATK4_SPLITNCIGARREADS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
gatk SplitNCigarReads \\
-R $fasta \\
-I $bam \\
-O ${prefix}.bam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gatk4/variantfiltration/functions.nf b/modules/gatk4/variantfiltration/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gatk4/variantfiltration/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf
index e0f0727a..d5cc1eb3 100644
--- a/modules/gatk4/variantfiltration/main.nf
+++ b/modules/gatk4/variantfiltration/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GATK4_VARIANTFILTRATION {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+ 'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(vcf_tbi)
@@ -30,7 +19,8 @@ process GATK4_VARIANTFILTRATION {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -42,11 +32,11 @@ process GATK4_VARIANTFILTRATION {
-R $fasta \\
-V $vcf \\
-O ${prefix}.vcf.gz \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+ "${task.process}":
+ gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/genmap/index/functions.nf b/modules/genmap/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/genmap/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/genmap/index/main.nf b/modules/genmap/index/main.nf
index c79596f0..943f1a31 100644
--- a/modules/genmap/index/main.nf
+++ b/modules/genmap/index/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GENMAP_INDEX {
tag '$fasta'
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1"
- } else {
- container "quay.io/biocontainers/genmap:1.3.0--h1b792b2_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' :
+ 'quay.io/biocontainers/genmap:1.3.0--h1b792b2_1' }"
input:
path fasta
@@ -26,6 +15,7 @@ process GENMAP_INDEX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
genmap \\
index \\
@@ -33,8 +23,8 @@ process GENMAP_INDEX {
-I genmap
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
+ "${task.process}":
+ genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/genmap/mappability/functions.nf b/modules/genmap/mappability/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/genmap/mappability/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/genmap/mappability/main.nf b/modules/genmap/mappability/main.nf
index 4d858cbb..94083f14 100644
--- a/modules/genmap/mappability/main.nf
+++ b/modules/genmap/mappability/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GENMAP_MAPPABILITY {
tag '$fasta'
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::genmap=1.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1"
- } else {
- container "quay.io/biocontainers/genmap:1.3.0--h1b792b2_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/genmap:1.3.0--h1b792b2_1' :
+ 'quay.io/biocontainers/genmap:1.3.0--h1b792b2_1' }"
input:
path index
@@ -28,16 +17,17 @@ process GENMAP_MAPPABILITY {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
genmap \\
map \\
- $options.args \\
+ $args \\
-I $index \\
-O mappability
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
+ "${task.process}":
+ genmap: \$(genmap --version 2>&1 | sed 's/GenMap version: //; s/SeqAn.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/genrich/functions.nf b/modules/genrich/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/genrich/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/genrich/main.nf b/modules/genrich/main.nf
index f34f9cd2..dfbebd3a 100644
--- a/modules/genrich/main.nf
+++ b/modules/genrich/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GENRICH {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::genrich=0.6.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1"
- } else {
- container "quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1' :
+ 'quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1' }"
input:
tuple val(meta), path(treatment_bam)
@@ -36,7 +25,8 @@ process GENRICH {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def control = control_bam ? "-c $control_bam" : ''
def blacklist = blacklist_bed ? "-E $blacklist_bed" : ""
def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
@@ -44,7 +34,7 @@ process GENRICH {
def bed = save_bed ? "-b ${prefix}.intervals.bed" : ""
def duplicates = ""
if (save_duplicates) {
- if (options.args.contains('-r')) {
+ if (args.contains('-r')) {
duplicates = "-R ${prefix}.duplicates.txt"
} else {
log.info '[Genrich] Duplicates can only be saved if they are filtered, defaulting to -r option (Remove PCR duplicates).'
@@ -54,7 +44,7 @@ process GENRICH {
"""
Genrich \\
-t $treatment_bam \\
- $options.args \\
+ $args \\
$control \\
$blacklist \\
-o ${prefix}.narrowPeak \\
@@ -65,8 +55,8 @@ process GENRICH {
$control
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
+ "${task.process}":
+ genrich: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gffread/functions.nf b/modules/gffread/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gffread/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gffread/main.nf b/modules/gffread/main.nf
index 4133ee08..d31f76f8 100644
--- a/modules/gffread/main.nf
+++ b/modules/gffread/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GFFREAD {
tag "$gff"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
- } else {
- container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' :
+ 'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }"
input:
path gff
@@ -26,15 +15,16 @@ process GFFREAD {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${gff.baseName}${options.suffix}" : "${gff.baseName}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${gff.baseName}${task.ext.suffix}" : "${gff.baseName}"
"""
gffread \\
$gff \\
- $options.args \\
+ $args \\
-o ${prefix}.gtf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(gffread --version 2>&1)
+ "${task.process}":
+ gffread: \$(gffread --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/glnexus/functions.nf b/modules/glnexus/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/glnexus/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/glnexus/main.nf b/modules/glnexus/main.nf
index 1384334f..e36729b2 100644
--- a/modules/glnexus/main.nf
+++ b/modules/glnexus/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GLNEXUS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0"
- } else {
- container "quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0' :
+ 'quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0' }"
input:
tuple val(meta), path(gvcfs)
@@ -26,7 +15,8 @@ process GLNEXUS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
// Make list of GVCFs to merge
def input = gvcfs.collect { it.toString() }
@@ -40,13 +30,13 @@ process GLNEXUS {
glnexus_cli \\
--threads $task.cpus \\
--mem-gbytes $avail_mem \\
- $options.args \\
+ $args \\
${input.join(' ')} \\
> ${prefix}.bcf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
+ "${task.process}":
+ glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/graphmap2/align/functions.nf b/modules/graphmap2/align/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/graphmap2/align/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/graphmap2/align/main.nf b/modules/graphmap2/align/main.nf
index 831b0b3b..e0f2d4cd 100644
--- a/modules/graphmap2/align/main.nf
+++ b/modules/graphmap2/align/main.nf
@@ -1,23 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GRAPHMAP2_ALIGN {
tag "$meta.id"
label 'process_medium'
tag "$meta.id"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0"
- } else {
- container "quay.io/biocontainers/graphmap:0.6.3--he513fc3_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' :
+ 'quay.io/biocontainers/graphmap:0.6.3--he513fc3_0' }"
input:
tuple val(meta), path(reads)
@@ -29,7 +18,8 @@ process GRAPHMAP2_ALIGN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
graphmap2 \\
align \\
@@ -38,11 +28,11 @@ process GRAPHMAP2_ALIGN {
-i $index \\
-d $reads \\
-o ${prefix}.sam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
+ "${task.process}":
+ graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/graphmap2/index/functions.nf b/modules/graphmap2/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/graphmap2/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/graphmap2/index/main.nf b/modules/graphmap2/index/main.nf
index a8b03074..fffc7bcb 100644
--- a/modules/graphmap2/index/main.nf
+++ b/modules/graphmap2/index/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GRAPHMAP2_INDEX {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:['']) }
conda (params.enable_conda ? "bioconda::graphmap=0.6.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0"
- } else {
- container "quay.io/biocontainers/graphmap:0.6.3--he513fc3_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/graphmap:0.6.3--he513fc3_0' :
+ 'quay.io/biocontainers/graphmap:0.6.3--he513fc3_0' }"
input:
path fasta
@@ -25,17 +14,18 @@ process GRAPHMAP2_INDEX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
graphmap2 \\
align \\
-t $task.cpus \\
-I \\
- $options.args \\
+ $args \\
-r $fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
+ "${task.process}":
+ graphmap2: \$(echo \$(graphmap2 align 2>&1) | sed 's/^.*Version: v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gstama/collapse/functions.nf b/modules/gstama/collapse/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gstama/collapse/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gstama/collapse/main.nf b/modules/gstama/collapse/main.nf
index 8fc7877f..d8a64113 100644
--- a/modules/gstama/collapse/main.nf
+++ b/modules/gstama/collapse/main.nf
@@ -1,23 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GSTAMA_COLLAPSE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0"
-
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' :
+ 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -37,17 +25,18 @@ process GSTAMA_COLLAPSE {
tuple val(meta), path("*_variants.txt") , emit: variants, optional: true
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
tama_collapse.py \\
-s $bam \\
-f $fasta \\
-p ${prefix} \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
+ "${task.process}":
+ gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
END_VERSIONS
"""
}
diff --git a/modules/gstama/merge/functions.nf b/modules/gstama/merge/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gstama/merge/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gstama/merge/main.nf b/modules/gstama/merge/main.nf
index 37d685f6..4a8e829c 100644
--- a/modules/gstama/merge/main.nf
+++ b/modules/gstama/merge/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GSTAMA_MERGE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' :
+ 'quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0' }"
input:
tuple val(meta), path(bed)
@@ -30,17 +19,18 @@ process GSTAMA_MERGE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
tama_merge.py \\
-f $filelist \\
-d merge_dup \\
-p ${prefix} \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( tama_merge.py -version | head -n1 )
+ "${task.process}":
+ gstama: \$( tama_merge.py -version | head -n1 )
END_VERSIONS
"""
}
diff --git a/modules/gtdbtk/classifywf/functions.nf b/modules/gtdbtk/classifywf/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gtdbtk/classifywf/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gtdbtk/classifywf/main.nf b/modules/gtdbtk/classifywf/main.nf
index fdcef76a..4a4b3a01 100644
--- a/modules/gtdbtk/classifywf/main.nf
+++ b/modules/gtdbtk/classifywf/main.nf
@@ -1,22 +1,12 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '1.5.0' // When using stubs for the GTDB database, the version info isn't printed.
+def VERSION = '1.5.0' // Version information not provided by tool on CLI
process GTDBTK_CLASSIFYWF {
tag "${meta.assembler}-${meta.id}"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' :
+ 'quay.io/biocontainers/gtdbtk:1.5.0--pyhdfd78af_0' }"
input:
tuple val(meta), path("bins/*")
@@ -35,6 +25,7 @@ process GTDBTK_CLASSIFYWF {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
"""
export GTDBTK_DATA_PATH="\${PWD}/database"
@@ -43,7 +34,7 @@ process GTDBTK_CLASSIFYWF {
fi
gtdbtk classify_wf \\
- $options.args \\
+ $args \\
--genome_dir bins \\
--prefix "gtdbtk.${meta.assembler}-${meta.id}" \\
--out_dir "\${PWD}" \\
@@ -58,8 +49,8 @@ process GTDBTK_CLASSIFYWF {
mv gtdbtk.warnings.log "gtdbtk.${meta.assembler}-${meta.id}.warnings.log"
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
+ "${task.process}":
+ gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
END_VERSIONS
"""
@@ -76,8 +67,8 @@ process GTDBTK_CLASSIFYWF {
touch gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo "$VERSION")
+ "${task.process}":
+ gtdbtk: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/gubbins/functions.nf b/modules/gubbins/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gubbins/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf
index da194906..b4c6dc23 100644
--- a/modules/gubbins/main.nf
+++ b/modules/gubbins/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GUBBINS {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::gubbins=3.0.0' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0"
- } else {
- container "quay.io/biocontainers/gubbins:3.0.0--py39h5bf99c6_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' :
+ 'quay.io/biocontainers/gubbins:3.0.0--py39h5bf99c6_0' }"
input:
path alignment
@@ -33,14 +22,15 @@ process GUBBINS {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
run_gubbins.py \\
--threads $task.cpus \\
- $options.args \\
+ $args \\
$alignment
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(run_gubbins.py --version 2>&1)
+ "${task.process}":
+ gubbins: \$(run_gubbins.py --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/gunc/downloaddb/functions.nf b/modules/gunc/downloaddb/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gunc/downloaddb/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gunc/downloaddb/main.nf b/modules/gunc/downloaddb/main.nf
index af421608..430b862b 100644
--- a/modules/gunc/downloaddb/main.nf
+++ b/modules/gunc/downloaddb/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GUNC_DOWNLOADDB {
tag '$db_name'
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
+ 'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
input:
val db_name
@@ -26,12 +15,13 @@ process GUNC_DOWNLOADDB {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
- gunc download_db . -db $db_name $options.args
+ gunc download_db . -db $db_name $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( gunc --version )
+ "${task.process}":
+ gunc: \$( gunc --version )
END_VERSIONS
"""
}
diff --git a/modules/gunc/run/functions.nf b/modules/gunc/run/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gunc/run/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gunc/run/main.nf b/modules/gunc/run/main.nf
index f873a7df..6ac681ad 100644
--- a/modules/gunc/run/main.nf
+++ b/modules/gunc/run/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GUNC_RUN {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0' :
+ 'quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0' }"
input:
tuple val(meta), path(fasta)
@@ -28,18 +17,19 @@ process GUNC_RUN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
gunc \\
run \\
--input_fasta $fasta \\
--db_file $db \\
--threads $task.cpus \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( gunc --version )
+ "${task.process}":
+ gunc: \$( gunc --version )
END_VERSIONS
"""
}
diff --git a/modules/gunzip/functions.nf b/modules/gunzip/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/gunzip/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf
index 564fa99d..77a4e546 100644
--- a/modules/gunzip/main.nf
+++ b/modules/gunzip/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process GUNZIP {
tag "$archive"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
- } else {
- container "biocontainers/biocontainers:v1.2.0_cv1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+ 'biocontainers/biocontainers:v1.2.0_cv1' }"
input:
tuple val(meta), path(archive)
@@ -26,16 +15,17 @@ process GUNZIP {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
gunzip = archive.toString() - '.gz'
"""
gunzip \\
-f \\
- $options.args \\
+ $args \\
$archive
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
+ "${task.process}":
+ gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/gunzip/test.txt.gz b/modules/gunzip/test.txt.gz
deleted file mode 100644
index 381417cf..00000000
Binary files a/modules/gunzip/test.txt.gz and /dev/null differ
diff --git a/modules/hicap/functions.nf b/modules/hicap/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hicap/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hicap/main.nf b/modules/hicap/main.nf
index fbc157b1..ed1d7797 100644
--- a/modules/hicap/main.nf
+++ b/modules/hicap/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process HICAP {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0"
- } else {
- container "quay.io/biocontainers/hicap:1.0.3--py_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0' :
+ 'quay.io/biocontainers/hicap:1.0.3--py_0' }"
input:
tuple val(meta), path(fasta)
@@ -30,7 +19,8 @@ process HICAP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def database_args = database_dir ? "--database_dir ${database_dir}" : ""
def model_args = model_fp ? "--model_fp ${model_fp}" : ""
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
@@ -43,13 +33,13 @@ process HICAP {
--query_fp $fasta_name \\
$database_args \\
$model_args \\
- $options.args \\
+ $args \\
--threads $task.cpus \\
-o ./
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$( hicap --version 2>&1 ) | sed 's/^.*hicap //' )
+ "${task.process}":
+ hicap: \$( echo \$( hicap --version 2>&1 ) | sed 's/^.*hicap //' )
END_VERSIONS
"""
}
diff --git a/modules/hifiasm/functions.nf b/modules/hifiasm/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hifiasm/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hifiasm/main.nf b/modules/hifiasm/main.nf
index 9dfc9618..7fc857f1 100644
--- a/modules/hifiasm/main.nf
+++ b/modules/hifiasm/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process HIFIASM {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::hifiasm=0.15.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/hifiasm:0.15.4--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hifiasm:0.15.4--h2e03b76_0' :
+ 'quay.io/biocontainers/hifiasm:0.15.4--h2e03b76_0' }"
input:
tuple val(meta), path(reads)
@@ -37,11 +26,12 @@ process HIFIASM {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (use_parental_kmers) {
"""
hifiasm \\
- $options.args \\
+ $args \\
-o ${prefix}.asm \\
-t $task.cpus \\
-1 $paternal_kmer_dump \\
@@ -49,21 +39,21 @@ process HIFIASM {
$reads
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(hifiasm --version 2>&1)
+ "${task.process}":
+ hifiasm: \$(hifiasm --version 2>&1)
END_VERSIONS
"""
} else { // Phasing with Hi-C data is not supported yet
"""
hifiasm \\
- $options.args \\
+ $args \\
-o ${prefix}.asm \\
-t $task.cpus \\
$reads
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(hifiasm --version 2>&1)
+ "${task.process}":
+ hifiasm: \$(hifiasm --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/hisat2/align/functions.nf b/modules/hisat2/align/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hisat2/align/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hisat2/align/main.nf b/modules/hisat2/align/main.nf
index 9b73216b..0c5f4134 100644
--- a/modules/hisat2/align/main.nf
+++ b/modules/hisat2/align/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '2.2.0'
+def VERSION = '2.2.0' // Version information not provided by tool on CLI
process HISAT2_ALIGN {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' :
+ 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0' }"
input:
tuple val(meta), path(reads)
@@ -26,14 +15,14 @@ process HISAT2_ALIGN {
path splicesites
output:
- tuple val(meta), path("*.bam"), emit: bam
- tuple val(meta), path("*.log"), emit: summary
- path "versions.yml" , emit: versions
-
+ tuple val(meta), path("*.bam") , emit: bam
+ tuple val(meta), path("*.log") , emit: summary
tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq
+ path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {
@@ -55,12 +44,12 @@ process HISAT2_ALIGN {
--threads $task.cpus \\
$seq_center \\
$unaligned \\
- $options.args \\
+ $args \\
| samtools view -bS -F 4 -F 256 - > ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ hisat2: $VERSION
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
@@ -80,7 +69,7 @@ process HISAT2_ALIGN {
$unaligned \\
--no-mixed \\
--no-discordant \\
- $options.args \\
+ $args \\
| samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
@@ -91,8 +80,8 @@ process HISAT2_ALIGN {
fi
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ hisat2: $VERSION
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
diff --git a/modules/hisat2/build/functions.nf b/modules/hisat2/build/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hisat2/build/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hisat2/build/main.nf b/modules/hisat2/build/main.nf
index 015f6f59..4e8cd02b 100644
--- a/modules/hisat2/build/main.nf
+++ b/modules/hisat2/build/main.nf
@@ -1,25 +1,14 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '2.2.0'
+def VERSION = '2.2.0' // Version information not provided by tool on CLI
process HISAT2_BUILD {
tag "$fasta"
label 'process_high'
label 'process_high_memory'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
- } else {
- container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
+ 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }"
input:
path fasta
@@ -31,6 +20,7 @@ process HISAT2_BUILD {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def avail_mem = 0
if (!task.memory) {
log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
@@ -52,7 +42,6 @@ process HISAT2_BUILD {
log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
}
-
"""
mkdir hisat2
$extract_exons
@@ -60,13 +49,13 @@ process HISAT2_BUILD {
-p $task.cpus \\
$ss \\
$exon \\
- $options.args \\
+ $args \\
$fasta \\
hisat2/${fasta.baseName}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ hisat2: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/hisat2/extractsplicesites/functions.nf b/modules/hisat2/extractsplicesites/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hisat2/extractsplicesites/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hisat2/extractsplicesites/main.nf b/modules/hisat2/extractsplicesites/main.nf
index 1c8b7830..302c35f1 100644
--- a/modules/hisat2/extractsplicesites/main.nf
+++ b/modules/hisat2/extractsplicesites/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '2.2.0'
+def VERSION = '2.2.0' // Version information not provided by tool on CLI
process HISAT2_EXTRACTSPLICESITES {
tag "$gtf"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
- } else {
- container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
+ 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }"
input:
path gtf
@@ -28,11 +17,12 @@ process HISAT2_EXTRACTSPLICESITES {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ hisat2: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/hmmcopy/gccounter/functions.nf b/modules/hmmcopy/gccounter/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hmmcopy/gccounter/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hmmcopy/gccounter/main.nf b/modules/hmmcopy/gccounter/main.nf
index 6e7bc11f..36666095 100644
--- a/modules/hmmcopy/gccounter/main.nf
+++ b/modules/hmmcopy/gccounter/main.nf
@@ -1,23 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '0.1.1'
+def VERSION = '0.1.1' // Version information not provided by tool on CLI
process HMMCOPY_GCCOUNTER {
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5"
- } else {
- container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5' :
+ 'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5' }"
input:
path fasta
@@ -27,14 +16,15 @@ process HMMCOPY_GCCOUNTER {
path "versions.yml", emit: versions
script:
+ def args = task.ext.args ?: ''
"""
gcCounter \\
- $options.args \\
+ $args \\
${fasta} > ${fasta.baseName}.gc.wig
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ hmmcopy: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/hmmcopy/readcounter/functions.nf b/modules/hmmcopy/readcounter/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hmmcopy/readcounter/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hmmcopy/readcounter/main.nf b/modules/hmmcopy/readcounter/main.nf
index 9e3e72a7..6cd776a1 100644
--- a/modules/hmmcopy/readcounter/main.nf
+++ b/modules/hmmcopy/readcounter/main.nf
@@ -1,42 +1,32 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '0.1.1'
+def VERSION = '0.1.1' // Version information not provided by tool on CLI
process HMMCOPY_READCOUNTER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5"
- } else {
- container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5' :
+ 'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5' }"
input:
- tuple val(meta), path(bam), path(bai)
+ tuple val(meta), path(bam), path(bai)
output:
- tuple val(meta), path("*.wig"), emit: wig
- path "versions.yml" , emit: versions
+ tuple val(meta), path("*.wig"), emit: wig
+ path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
readCounter \\
- $options.args \\
+ $args \\
${bam} > ${prefix}.wig
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ hmmcopy: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/hmmer/hmmalign/functions.nf b/modules/hmmer/hmmalign/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/hmmer/hmmalign/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/hmmer/hmmalign/main.nf b/modules/hmmer/hmmalign/main.nf
index b4292feb..a25871e8 100644
--- a/modules/hmmer/hmmalign/main.nf
+++ b/modules/hmmer/hmmalign/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process HMMER_HMMALIGN {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1"
- } else {
- container "quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' :
+ 'quay.io/biocontainers/hmmer:3.3.2--h1b792b2_1' }"
input:
tuple val(meta), path(fasta)
@@ -27,18 +16,19 @@ process HMMER_HMMALIGN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def fastacmd = fasta.getExtension() == 'gz' ? "gunzip -c $fasta" : "cat $fasta"
"""
$fastacmd | \\
hmmalign \\
- $options.args \\
+ $args \\
$hmm \\
- | gzip -c > ${meta.id}.sthlm.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
+ "${task.process}":
+ hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
END_VERSIONS
"""
}
diff --git a/modules/homer/annotatepeaks/functions.nf b/modules/homer/annotatepeaks/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/homer/annotatepeaks/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/homer/annotatepeaks/main.nf b/modules/homer/annotatepeaks/main.nf
index 1714644b..321dbc7c 100644
--- a/modules/homer/annotatepeaks/main.nf
+++ b/modules/homer/annotatepeaks/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '4.11'
+def VERSION = '4.11' // Version information not provided by tool on CLI
process HOMER_ANNOTATEPEAKS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::homer=4.11" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
- } else {
- container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
+ 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(peak)
@@ -30,19 +19,20 @@ process HOMER_ANNOTATEPEAKS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
annotatePeaks.pl \\
$peak \\
$fasta \\
- $options.args \\
+ $args \\
-gtf $gtf \\
-cpu $task.cpus \\
> ${prefix}.annotatePeaks.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ homer: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/homer/findpeaks/functions.nf b/modules/homer/findpeaks/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/homer/findpeaks/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/homer/findpeaks/main.nf b/modules/homer/findpeaks/main.nf
index 2e0b6db9..a39fe753 100644
--- a/modules/homer/findpeaks/main.nf
+++ b/modules/homer/findpeaks/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-def options = initOptions(params.options)
-
-def VERSION = '4.11'
+def VERSION = '4.11' // Version information not provided by tool on CLI
process HOMER_FINDPEAKS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
- } else {
- container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
+ 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(tagDir)
@@ -28,17 +17,18 @@ process HOMER_FINDPEAKS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
findPeaks \\
$tagDir \\
- $options.args \\
+ $args \\
-o ${prefix}.peaks.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ homer: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/homer/maketagdirectory/functions.nf b/modules/homer/maketagdirectory/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/homer/maketagdirectory/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/homer/maketagdirectory/main.nf b/modules/homer/maketagdirectory/main.nf
index 4f531e82..44490d50 100644
--- a/modules/homer/maketagdirectory/main.nf
+++ b/modules/homer/maketagdirectory/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-def options = initOptions(params.options)
-
-def VERSION = '4.11'
+def VERSION = '4.11' // Version information not provided by tool on CLI
process HOMER_MAKETAGDIRECTORY {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
- } else {
- container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
+ 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(bed)
@@ -26,20 +15,21 @@ process HOMER_MAKETAGDIRECTORY {
output:
tuple val(meta), path("tag_dir"), emit: tagdir
- path "versions.yml" , emit: versions
+ path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
makeTagDirectory \\
tag_dir \\
- $options.args \\
+ $args \\
$bed \\
-genome $fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ homer: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/homer/makeucscfile/functions.nf b/modules/homer/makeucscfile/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/homer/makeucscfile/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/homer/makeucscfile/main.nf b/modules/homer/makeucscfile/main.nf
index c56da24b..8a0e3f37 100644
--- a/modules/homer/makeucscfile/main.nf
+++ b/modules/homer/makeucscfile/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-def options = initOptions(params.options)
-
-def VERSION = '4.11'
+def VERSION = '4.11' // Version information not provided by tool on CLI
process HOMER_MAKEUCSCFILE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3"
- } else {
- container "quay.io/biocontainers/homer:4.11--pl526hc9558a2_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
+ 'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(tagDir)
@@ -28,16 +17,17 @@ process HOMER_MAKEUCSCFILE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
makeUCSCfile \\
$tagDir \\
- -o auto
- $options.args
+ -o auto \\
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ homer: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/idr/functions.nf b/modules/idr/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/idr/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/idr/main.nf b/modules/idr/main.nf
index 006826ac..44b07be4 100644
--- a/modules/idr/main.nf
+++ b/modules/idr/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process IDR {
tag "$prefix"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5"
- } else {
- container "quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' :
+ 'quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5' }"
input:
path peaks
@@ -30,6 +19,7 @@ process IDR {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
if (peaks.toList().size < 2) {
log.error "[ERROR] idr needs at least two replicates only one provided."
}
@@ -46,11 +36,11 @@ process IDR {
--output-file $idr_vals \\
--log-output-file $log_file \\
--plot \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//')
+ "${task.process}":
+ idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/imputeme/vcftoprs/functions.nf b/modules/imputeme/vcftoprs/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/imputeme/vcftoprs/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/imputeme/vcftoprs/main.nf b/modules/imputeme/vcftoprs/main.nf
index a3ce7e3c..0c8c1952 100644
--- a/modules/imputeme/vcftoprs/main.nf
+++ b/modules/imputeme/vcftoprs/main.nf
@@ -1,23 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-
-params.options = [:]
-options = initOptions(params.options)
-
process IMPUTEME_VCFTOPRS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "YOUR-TOOL-HERE" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img"
- } else {
- container "biocontainers/imputeme:vv1.0.7_cv1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img' :
+ 'biocontainers/imputeme:vv1.0.7_cv1' }"
input:
tuple val(meta), path(vcf)
@@ -27,14 +15,15 @@ process IMPUTEME_VCFTOPRS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
#!/usr/bin/env Rscript
- #Set configuration - either from options.args or from defaults
+ #Set configuration - either from args or from defaults
source("/imputeme/code/impute-me/functions.R")
- if(file.exists('$options.args')){
- set_conf("set_from_file",'$options.args')
+ if(file.exists('$args')){
+ set_conf("set_from_file",'$args')
}else{
set_conf("set_from_file", "/imputeme/code/impute-me/template/nextflow_default_configuration.R")
}
diff --git a/modules/iqtree/functions.nf b/modules/iqtree/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/iqtree/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/iqtree/main.nf b/modules/iqtree/main.nf
index bec879df..54a6486d 100644
--- a/modules/iqtree/main.nf
+++ b/modules/iqtree/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process IQTREE {
tag "$alignment"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0"
- } else {
- container "quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0' :
+ 'quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0' }"
input:
path alignment
@@ -27,20 +16,21 @@ process IQTREE {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
def memory = task.memory.toString().replaceAll(' ', '')
"""
iqtree \\
$fconst_args \\
- $options.args \\
+ $args \\
-s $alignment \\
-nt AUTO \\
-ntmax $task.cpus \\
-mem $memory \\
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
+ "${task.process}":
+ iqtree: \$(echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version //;s/ .*//')
END_VERSIONS
"""
}
diff --git a/modules/ismapper/functions.nf b/modules/ismapper/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ismapper/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ismapper/main.nf b/modules/ismapper/main.nf
index 20d3d5b7..4a33261b 100644
--- a/modules/ismapper/main.nf
+++ b/modules/ismapper/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process ISMAPPER {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1"
- } else {
- container "quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' :
+ 'quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(reads), path(reference), path(query)
@@ -26,10 +15,11 @@ process ISMAPPER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
ismap \\
- $options.args \\
+ $args \\
--t $task.cpus \\
--output_dir results \\
--queries $query \\
@@ -37,8 +27,8 @@ process ISMAPPER {
--reads $reads
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$( ismap --version 2>&1 ) | sed 's/^.*ismap //' )
+ "${task.process}":
+ ismapper: \$( echo \$( ismap --version 2>&1 ) | sed 's/^.*ismap //' )
END_VERSIONS
"""
}
diff --git a/modules/isoseq3/cluster/functions.nf b/modules/isoseq3/cluster/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/isoseq3/cluster/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/isoseq3/cluster/main.nf b/modules/isoseq3/cluster/main.nf
index df005706..27d5c3d8 100644
--- a/modules/isoseq3/cluster/main.nf
+++ b/modules/isoseq3/cluster/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process ISOSEQ3_CLUSTER {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0"
- } else {
- container "quay.io/biocontainers/isoseq3:3.4.0--0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' :
+ 'quay.io/biocontainers/isoseq3:3.4.0--0' }"
input:
tuple val(meta), path(bam)
@@ -27,28 +16,27 @@ process ISOSEQ3_CLUSTER {
tuple val(meta), path("*.transcripts.cluster") , emit: cluster
tuple val(meta), path("*.transcripts.cluster_report.csv"), emit: cluster_report
tuple val(meta), path("*.transcripts.transcriptset.xml") , emit: transcriptset
- path "versions.yml" , emit: versions
-
tuple val(meta), path("*.transcripts.hq.bam") , optional: true, emit: hq_bam
tuple val(meta), path("*.transcripts.hq.bam.pbi") , optional: true, emit: hq_pbi
tuple val(meta), path("*.transcripts.lq.bam") , optional: true, emit: lq_bam
tuple val(meta), path("*.transcripts.lq.bam.pbi") , optional: true, emit: lq_pbi
tuple val(meta), path("*.transcripts.singletons.bam") , optional: true, emit: singletons_bam
tuple val(meta), path("*.transcripts.singletons.bam.pbi"), optional: true, emit: singletons_pbi
-
+ path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
isoseq3 \\
cluster \\
$bam \\
${prefix}.transcripts.bam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- isoseq3 cluster: \$( isoseq3 cluster --version|sed 's/isoseq cluster //g'|sed 's/ (.*//g' )
+ "${task.process}":
+ isoseq3: \$( isoseq3 cluster --version|sed 's/isoseq cluster //g'|sed 's/ (.*//g' )
END_VERSIONS
"""
}
diff --git a/modules/isoseq3/refine/functions.nf b/modules/isoseq3/refine/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/isoseq3/refine/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/isoseq3/refine/main.nf b/modules/isoseq3/refine/main.nf
index 5a45eb2d..5bde2f8f 100644
--- a/modules/isoseq3/refine/main.nf
+++ b/modules/isoseq3/refine/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process ISOSEQ3_REFINE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0"
- } else {
- container "quay.io/biocontainers/isoseq3:3.4.0--0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' :
+ 'quay.io/biocontainers/isoseq3:3.4.0--0' }"
input:
tuple val(meta), path(bam)
@@ -31,19 +20,20 @@ process ISOSEQ3_REFINE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
isoseq3 \\
refine \\
-j $task.cpus \\
- $options.args \\
+ $args \\
$bam \\
$primers \\
${prefix}.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( isoseq3 refine --version|sed 's/isoseq refine //'|sed 's/ (commit.\\+//' )
+ "${task.process}":
+ isoseq3: \$( isoseq3 refine --version|sed 's/isoseq refine //'|sed 's/ (commit.\\+//' )
END_VERSIONS
"""
}
diff --git a/modules/ivar/consensus/functions.nf b/modules/ivar/consensus/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ivar/consensus/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ivar/consensus/main.nf b/modules/ivar/consensus/main.nf
index 33fa11f7..4a657756 100644
--- a/modules/ivar/consensus/main.nf
+++ b/modules/ivar/consensus/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process IVAR_CONSENSUS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
- } else {
- container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' :
+ 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }"
input:
tuple val(meta), path(bam)
@@ -29,21 +18,23 @@ process IVAR_CONSENSUS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
"""
samtools mpileup \\
--reference $fasta \\
- $options.args2 \\
+ $args2 \\
$bam | \\
$save_mpileup \\
ivar consensus \\
- $options.args \\
+ $args \\
-p $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
+ "${task.process}":
+ ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/ivar/trim/functions.nf b/modules/ivar/trim/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ivar/trim/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ivar/trim/main.nf b/modules/ivar/trim/main.nf
index 6cf8171c..35798123 100644
--- a/modules/ivar/trim/main.nf
+++ b/modules/ivar/trim/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process IVAR_TRIM {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
- } else {
- container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' :
+ 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -28,18 +17,19 @@ process IVAR_TRIM {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
ivar trim \\
- $options.args \\
+ $args \\
-i $bam \\
-b $bed \\
-p $prefix \\
> ${prefix}.ivar.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
+ "${task.process}":
+ ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/ivar/variants/functions.nf b/modules/ivar/variants/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ivar/variants/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ivar/variants/main.nf b/modules/ivar/variants/main.nf
index d079a8e9..ba791307 100644
--- a/modules/ivar/variants/main.nf
+++ b/modules/ivar/variants/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process IVAR_VARIANTS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
- } else {
- container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0' :
+ 'quay.io/biocontainers/ivar:1.3.1--h089eab3_0' }"
input:
tuple val(meta), path(bam)
@@ -29,24 +18,26 @@ process IVAR_VARIANTS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
def features = params.gff ? "-g $gff" : ""
"""
samtools mpileup \\
- $options.args2 \\
+ $args2 \\
--reference $fasta \\
$bam | \\
$save_mpileup \\
ivar variants \\
- $options.args \\
+ $args \\
$features \\
-r $fasta \\
-p $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
+ "${task.process}":
+ ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/jupyternotebook/functions.nf b/modules/jupyternotebook/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/jupyternotebook/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/jupyternotebook/main.nf b/modules/jupyternotebook/main.nf
index 2d8ad92f..02f1947f 100644
--- a/modules/jupyternotebook/main.nf
+++ b/modules/jupyternotebook/main.nf
@@ -1,29 +1,16 @@
-// Import generic module functions
-include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
include { dump_params_yml; indent_code_block } from "./parametrize"
-params.options = [:]
-options = initOptions(params.options)
-params.parametrize = true
-params.implicit_params = true
-params.meta_params = true
-
process JUPYTERNOTEBOOK {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
//NB: You likely want to override this with a container containing all required
//dependencies for your analysis. The container at least needs to contain the
//ipykernel, jupytext, papermill and nbconvert Python packages.
conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
+ 'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
input:
tuple val(meta), path(notebook)
@@ -36,7 +23,11 @@ process JUPYTERNOTEBOOK {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize
+ def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
+ def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
// Dump parameters to yaml file.
// Using a yaml file over using the CLI params because
@@ -44,14 +35,14 @@ process JUPYTERNOTEBOOK {
// * allows to pass nested maps instead of just single values
def params_cmd = ""
def render_cmd = ""
- if (params.parametrize) {
+ if (parametrize) {
nb_params = [:]
- if (params.implicit_params) {
+ if (implicit_params) {
nb_params["cpus"] = task.cpus
nb_params["artifact_dir"] = "artifacts"
nb_params["input_dir"] = "./"
}
- if (params.meta_params) {
+ if (meta_params) {
nb_params["meta"] = meta
}
nb_params += parameters
@@ -71,10 +62,10 @@ process JUPYTERNOTEBOOK {
mkdir artifacts
# Set parallelism for BLAS/MKL etc. to avoid over-booking of resources
- export MKL_NUM_THREADS="${task.cpus}"
- export OPENBLAS_NUM_THREADS="${task.cpus}"
- export OMP_NUM_THREADS="${task.cpus}"
- export NUMBA_NUM_THREADS="${task.cpus}"
+ export MKL_NUM_THREADS="$task.cpus"
+ export OPENBLAS_NUM_THREADS="$task.cpus"
+ export OMP_NUM_THREADS="$task.cpus"
+ export NUMBA_NUM_THREADS="$task.cpus"
# Convert notebook to ipynb using jupytext, execute using papermill, convert using nbconvert
jupytext --to notebook --output - --set-kernel - ${notebook} \\
@@ -82,7 +73,7 @@ process JUPYTERNOTEBOOK {
| jupyter nbconvert --stdin --to html --output ${prefix}.html
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
+ "${task.process}":
jupytext: \$(jupytext --version)
ipykernel: \$(python -c "import ipykernel; print(ipykernel.__version__)")
nbconvert: \$(jupyter nbconvert --version)
diff --git a/modules/kallisto/index/functions.nf b/modules/kallisto/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kallisto/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kallisto/index/main.nf b/modules/kallisto/index/main.nf
index 96457b6d..4dc9c6d0 100644
--- a/modules/kallisto/index/main.nf
+++ b/modules/kallisto/index/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process KALLISTO_INDEX {
tag "$fasta"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::kallisto=0.46.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1"
- } else {
- container "quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' :
+ 'quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1' }"
input:
path fasta
@@ -26,16 +15,17 @@ process KALLISTO_INDEX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
kallisto \\
index \\
- $options.args \\
+ $args \\
-i kallisto \\
$fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
+ "${task.process}":
+ kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/kallistobustools/count/functions.nf b/modules/kallistobustools/count/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kallistobustools/count/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf
index 8c705e51..00ca8971 100644
--- a/modules/kallistobustools/count/main.nf
+++ b/modules/kallistobustools/count/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process KALLISTOBUSTOOLS_COUNT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0' :
+ 'quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0' }"
input:
tuple val(meta), path(reads)
@@ -24,7 +13,7 @@ process KALLISTOBUSTOOLS_COUNT {
path t2g
path t1c
path t2c
- val workflow
+ val workflow_mode
val technology
output:
@@ -32,7 +21,8 @@ process KALLISTOBUSTOOLS_COUNT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def cdna = t1c ? "-c1 $t1c" : ''
def introns = t2c ? "-c2 $t2c" : ''
"""
@@ -43,16 +33,16 @@ process KALLISTOBUSTOOLS_COUNT {
-g $t2g \\
$cdna \\
$introns \\
- --workflow $workflow \\
+ --workflow $workflow_mode \\
-x $technology \\
- $options.args \\
+ $args \\
-o ${prefix}.count \\
${reads[0]} \\
${reads[1]}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+ "${task.process}":
+ kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/kallistobustools/count/meta.yml b/modules/kallistobustools/count/meta.yml
index bc2433bb..911697d2 100644
--- a/modules/kallistobustools/count/meta.yml
+++ b/modules/kallistobustools/count/meta.yml
@@ -39,9 +39,9 @@ input:
type: file
description: kb ref's c2 unspliced_t2c file
pattern: "*.{introns_t2c.txt}"
- - workflow:
+ - workflow_mode:
type: value
- description: String value defining worfklow to use, can be one of "standard", "lamanno", "nucleus"
+ description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
pattern: "{standard,lamanno,nucleus,kite}"
- technology:
type: value
diff --git a/modules/kallistobustools/ref/functions.nf b/modules/kallistobustools/ref/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kallistobustools/ref/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kallistobustools/ref/main.nf b/modules/kallistobustools/ref/main.nf
index a8287498..1e496f67 100644
--- a/modules/kallistobustools/ref/main.nf
+++ b/modules/kallistobustools/ref/main.nf
@@ -1,27 +1,16 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process KALLISTOBUSTOOLS_REF {
tag "$fasta"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::kb-python=0.26.3' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0' :
+ 'quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0' }"
input:
path fasta
path gtf
- val workflow
+ val workflow_mode
output:
path "versions.yml" , emit: versions
@@ -33,20 +22,21 @@ process KALLISTOBUSTOOLS_REF {
path "intron_t2c.txt" , optional:true, emit: intron_t2c
script:
- if (workflow == "standard") {
+ def args = task.ext.args ?: ''
+ if (workflow_mode == "standard") {
"""
kb \\
ref \\
-i kb_ref_out.idx \\
-g t2g.txt \\
-f1 cdna.fa \\
- --workflow $workflow \\
+ --workflow $workflow_mode \\
$fasta \\
$gtf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+ "${task.process}":
+ kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
END_VERSIONS
"""
} else {
@@ -59,13 +49,13 @@ process KALLISTOBUSTOOLS_REF {
-f2 intron.fa \\
-c1 cdna_t2c.txt \\
-c2 intron_t2c.txt \\
- --workflow $workflow \\
+ --workflow $workflow_mode \\
$fasta \\
$gtf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
+ "${task.process}":
+ kallistobustools: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/kallistobustools/ref/meta.yml b/modules/kallistobustools/ref/meta.yml
index 353b9c11..dcc78c66 100644
--- a/modules/kallistobustools/ref/meta.yml
+++ b/modules/kallistobustools/ref/meta.yml
@@ -21,9 +21,9 @@ input:
type: file
description: Genomic gtf file
pattern: "*.{gtf,gtf.gz}"
- - workflow:
+ - workflow_mode:
type: value
- description: String value defining worfklow to use, can be one of "standard", "lamanno", "nucleus"
+ description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus"
pattern: "{standard,lamanno,nucleus}"
output:
diff --git a/modules/khmer/normalizebymedian/functions.nf b/modules/khmer/normalizebymedian/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/khmer/normalizebymedian/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/khmer/normalizebymedian/main.nf b/modules/khmer/normalizebymedian/main.nf
index 234d172b..50b3d603 100644
--- a/modules/khmer/normalizebymedian/main.nf
+++ b/modules/khmer/normalizebymedian/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process KHMER_NORMALIZEBYMEDIAN {
tag "${name}"
label 'process_long'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2"
- } else {
- container "quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' :
+ 'quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
input:
path pe_reads
@@ -28,22 +17,22 @@ process KHMER_NORMALIZEBYMEDIAN {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
pe_args = pe_reads ? "--paired" : ""
se_args = se_reads ? "--unpaired-reads ${se_reads}" : ""
files = pe_reads ? pe_reads : se_reads
-
"""
normalize-by-median.py \\
-M ${task.memory.toGiga()}e9 \\
- --gzip ${options.args} \\
+ --gzip $args \\
-o ${name}.fastq.gz \\
- ${pe_args} \\
- ${se_args} \\
- ${files}
+ $pe_args \\
+ $se_args \\
+ $files
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( normalize-by-median.py --version 2>&1 | grep ^khmer | sed 's/^khmer //' )
+ "${task.process}":
+ khmer: \$( normalize-by-median.py --version 2>&1 | grep ^khmer | sed 's/^khmer //' )
END_VERSIONS
"""
}
diff --git a/modules/kleborate/functions.nf b/modules/kleborate/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kleborate/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kleborate/main.nf b/modules/kleborate/main.nf
index 5bb76ad0..b64a0c45 100644
--- a/modules/kleborate/main.nf
+++ b/modules/kleborate/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process KLEBORATE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1"
- } else {
- container "quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' :
+ 'quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1' }"
input:
tuple val(meta), path(fastas)
@@ -26,16 +15,17 @@ process KLEBORATE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
kleborate \\
- $options.args \\
+ $args \\
--outfile ${prefix}.results.txt \\
--assemblies *.fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(kleborate --version | sed 's/Kleborate v//;'))
+ "${task.process}":
+ kleborate: \$( echo \$(kleborate --version | sed 's/Kleborate v//;'))
END_VERSIONS
"""
}
diff --git a/modules/kraken2/kraken2/functions.nf b/modules/kraken2/kraken2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kraken2/kraken2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kraken2/kraken2/main.nf b/modules/kraken2/kraken2/main.nf
index 0d4e5840..e5fb4b80 100644
--- a/modules/kraken2/kraken2/main.nf
+++ b/modules/kraken2/kraken2/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process KRAKEN2_KRAKEN2 {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::kraken2=2.1.1 conda-forge::pigz=2.6' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
- } else {
- container 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' :
+ 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' }"
input:
tuple val(meta), path(reads)
@@ -29,7 +18,8 @@ process KRAKEN2_KRAKEN2 {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def paired = meta.single_end ? "" : "--paired"
def classified = meta.single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
def unclassified = meta.single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
@@ -42,14 +32,14 @@ process KRAKEN2_KRAKEN2 {
--report ${prefix}.kraken2.report.txt \\
--gzip-compressed \\
$paired \\
- $options.args \\
+ $args \\
$reads
pigz -p $task.cpus *.fastq
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
+ "${task.process}":
+ kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
diff --git a/modules/krona/kronadb/main.nf b/modules/krona/kronadb/main.nf
new file mode 100644
index 00000000..ca7fc3d3
--- /dev/null
+++ b/modules/krona/kronadb/main.nf
@@ -0,0 +1,27 @@
+def VERSION='2.7.1' // Version information not provided by tool on CLI
+
+process KRONA_KRONADB {
+ label 'process_low'
+
+ conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
+ 'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
+
+ input:
+
+ output:
+ path 'taxonomy/taxonomy.tab', emit: db
+ path "versions.yml" , emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ ktUpdateTaxonomy.sh taxonomy
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ krona: $VERSION
+ END_VERSIONS
+ """
+}
diff --git a/modules/kronatools/kronadb/meta.yml b/modules/krona/kronadb/meta.yml
similarity index 95%
rename from modules/kronatools/kronadb/meta.yml
rename to modules/krona/kronadb/meta.yml
index 5a637949..2a12aaaf 100644
--- a/modules/kronatools/kronadb/meta.yml
+++ b/modules/krona/kronadb/meta.yml
@@ -1,11 +1,11 @@
-name: kronatools_kronadb
+name: krona_kronadb
description: KronaTools Update Taxonomy downloads a taxonomy database
keywords:
- database
- taxonomy
- krona
tools:
- - kronatools:
+ - krona:
description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
homepage: https://github.com/marbl/Krona/wiki/KronaTools
documentation: https://github.com/marbl/Krona/wiki/Installing
diff --git a/modules/krona/ktimporttaxonomy/main.nf b/modules/krona/ktimporttaxonomy/main.nf
new file mode 100644
index 00000000..bc79c98c
--- /dev/null
+++ b/modules/krona/ktimporttaxonomy/main.nf
@@ -0,0 +1,30 @@
+def VERSION = '2.8' // Version information not provided by tool on CLI
+
+process KRONA_KTIMPORTTAXONOMY {
+ tag "${meta.id}"
+ label 'process_high'
+
+ conda (params.enable_conda ? "bioconda::krona=2.8" : null)
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
+ 'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"
+
+ input:
+ tuple val(meta), path(report)
+ path "taxonomy/taxonomy.tab"
+
+ output:
+ tuple val(meta), path ('*.html'), emit: html
+ path "versions.yml" , emit: versions
+
+ script:
+ def args = task.ext.args ?: ''
+ """
+ ktImportTaxonomy "$report" -tax taxonomy
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ krona: $VERSION
+ END_VERSIONS
+ """
+}
diff --git a/modules/kronatools/ktimporttaxonomy/meta.yml b/modules/krona/ktimporttaxonomy/meta.yml
similarity index 95%
rename from modules/kronatools/ktimporttaxonomy/meta.yml
rename to modules/krona/ktimporttaxonomy/meta.yml
index f37f2db4..b65919f8 100644
--- a/modules/kronatools/ktimporttaxonomy/meta.yml
+++ b/modules/krona/ktimporttaxonomy/meta.yml
@@ -1,4 +1,4 @@
-name: kronatools_ktimporttaxonomy
+name: krona_ktimporttaxonomy
description: KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot.
keywords:
- plot
@@ -8,7 +8,7 @@ keywords:
- visualisation
- krona chart
tools:
- - kronatools:
+ - krona:
description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
homepage: https://github.com/marbl/Krona/wiki/KronaTools
documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
@@ -24,7 +24,7 @@ input:
e.g. [ id:'test']
- database:
type: path
- description: "Path to the taxonomy database downloaded by kronatools/kronadb"
+ description: "Path to the taxonomy database downloaded by krona/kronadb"
- report:
type: file
description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored."
diff --git a/modules/kronatools/kronadb/functions.nf b/modules/kronatools/kronadb/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kronatools/kronadb/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kronatools/kronadb/main.nf b/modules/kronatools/kronadb/main.nf
deleted file mode 100644
index 7dee12d0..00000000
--- a/modules/kronatools/kronadb/main.nf
+++ /dev/null
@@ -1,35 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-process KRONATOOLS_KRONADB {
- label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
-
- conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5"
- } else {
- container "quay.io/biocontainers/krona:2.7.1--pl526_5"
- }
- input:
-
- output:
- path 'taxonomy/taxonomy.tab', emit: db
- path "versions.yml" , emit: versions
-
- script:
- def VERSION='2.7.1'
- """
- ktUpdateTaxonomy.sh taxonomy
-
- cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: $VERSION
- END_VERSIONS
- """
-}
diff --git a/modules/kronatools/ktimporttaxonomy/functions.nf b/modules/kronatools/ktimporttaxonomy/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/kronatools/ktimporttaxonomy/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/kronatools/ktimporttaxonomy/main.nf b/modules/kronatools/ktimporttaxonomy/main.nf
deleted file mode 100644
index 893bc5b2..00000000
--- a/modules/kronatools/ktimporttaxonomy/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-process KRONATOOLS_KTIMPORTTAXONOMY {
- tag "${meta.id}"
- label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
-
- conda (params.enable_conda ? "bioconda::krona=2.8" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2"
- } else {
- container "quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2"
- }
-
- input:
- tuple val(meta), path(report)
- path "taxonomy/taxonomy.tab"
-
- output:
- tuple val(meta), path ('*.html'), emit: html
- path "versions.yml" , emit: versions
-
- script:
- def VERSION='2.8'
- """
- ktImportTaxonomy "$report" -tax taxonomy
-
- cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: $VERSION
- END_VERSIONS
- """
-}
diff --git a/modules/last/dotplot/functions.nf b/modules/last/dotplot/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/dotplot/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/dotplot/main.nf b/modules/last/dotplot/main.nf
index d02e98ad..51667378 100644
--- a/modules/last/dotplot/main.nf
+++ b/modules/last/dotplot/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_DOTPLOT {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(maf)
@@ -28,17 +17,18 @@ process LAST_DOTPLOT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
last-dotplot \\
- $options.args \\
+ $args \\
$maf \\
$prefix.$format
# last-dotplot has no --version option so let's use lastal from the same suite
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastal --version | sed 's/lastal //')
+ "${task.process}":
+ last: \$(lastal --version | sed 's/lastal //')
END_VERSIONS
"""
}
diff --git a/modules/last/lastal/functions.nf b/modules/last/lastal/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/lastal/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/lastal/main.nf b/modules/last/lastal/main.nf
index c4335f25..4b90a965 100644
--- a/modules/last/lastal/main.nf
+++ b/modules/last/lastal/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_LASTAL {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(fastx), path (param_file)
@@ -27,13 +16,14 @@ process LAST_LASTAL {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def trained_params = param_file ? "-p ${param_file}" : ''
"""
INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
lastal \\
$trained_params \\
- $options.args \\
+ $args \\
-P $task.cpus \\
${index}/\$INDEX_NAME \\
$fastx \\
@@ -42,8 +32,8 @@ process LAST_LASTAL {
# which makes its checksum non-reproducible.
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastal --version 2>&1 | sed 's/lastal //')
+ "${task.process}":
+ last: \$(lastal --version 2>&1 | sed 's/lastal //')
END_VERSIONS
"""
}
diff --git a/modules/last/lastdb/functions.nf b/modules/last/lastdb/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/lastdb/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/lastdb/main.nf b/modules/last/lastdb/main.nf
index fb765ada..ff6485dc 100644
--- a/modules/last/lastdb/main.nf
+++ b/modules/last/lastdb/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_LASTDB {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(fastx)
@@ -26,18 +15,19 @@ process LAST_LASTDB {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mkdir lastdb
lastdb \\
- $options.args \\
+ $args \\
-P $task.cpus \\
lastdb/${prefix} \\
$fastx
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //')
+ "${task.process}":
+ last: \$(lastdb --version 2>&1 | sed 's/lastdb //')
END_VERSIONS
"""
}
diff --git a/modules/last/mafconvert/functions.nf b/modules/last/mafconvert/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/mafconvert/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/mafconvert/main.nf b/modules/last/mafconvert/main.nf
index 5e259109..f1a7312e 100644
--- a/modules/last/mafconvert/main.nf
+++ b/modules/last/mafconvert/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_MAFCONVERT {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(maf)
@@ -35,15 +24,16 @@ process LAST_MAFCONVERT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- maf-convert $options.args $format $maf | gzip --no-name \\
+ maf-convert $args $format $maf | gzip --no-name \\
> ${prefix}.${format}.gz
# maf-convert has no --version option but lastdb (part of the same package) has.
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //')
+ "${task.process}":
+ last: \$(lastdb --version 2>&1 | sed 's/lastdb //')
END_VERSIONS
"""
}
diff --git a/modules/last/mafswap/functions.nf b/modules/last/mafswap/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/mafswap/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/mafswap/main.nf b/modules/last/mafswap/main.nf
index 5ce38c92..c66e47d4 100644
--- a/modules/last/mafswap/main.nf
+++ b/modules/last/mafswap/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_MAFSWAP {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(maf)
@@ -26,14 +15,15 @@ process LAST_MAFSWAP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- maf-swap $options.args $maf | gzip --no-name > ${prefix}.swapped.maf.gz
+ maf-swap $args $maf | gzip --no-name > ${prefix}.swapped.maf.gz
# maf-swap has no --version option but lastdb, part of the same package, has.
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastdb --version 2>&1 | sed 's/lastdb //')
+ "${task.process}":
+ last: \$(lastdb --version 2>&1 | sed 's/lastdb //')
END_VERSIONS
"""
}
diff --git a/modules/last/postmask/functions.nf b/modules/last/postmask/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/postmask/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf
index 3102fbe6..e4f4390a 100644
--- a/modules/last/postmask/main.nf
+++ b/modules/last/postmask/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_POSTMASK {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(maf)
@@ -26,15 +15,16 @@ process LAST_POSTMASK {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate"
"""
- last-postmask $options.args $maf | gzip --no-name > ${prefix}.maf.gz
+ last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz
# last-postmask does not have a --version option
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastal --version 2>&1 | sed 's/lastal //')
+ "${task.process}":
+ last: \$(lastal --version 2>&1 | sed 's/lastal //')
END_VERSIONS
"""
}
diff --git a/modules/last/split/functions.nf b/modules/last/split/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/split/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/split/main.nf b/modules/last/split/main.nf
index 2a9e5621..ecc47e80 100644
--- a/modules/last/split/main.nf
+++ b/modules/last/split/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_SPLIT {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(maf)
@@ -26,13 +15,14 @@ process LAST_SPLIT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- zcat < $maf | last-split $options.args | gzip --no-name > ${prefix}.maf.gz
+ zcat < $maf | last-split $args | gzip --no-name > ${prefix}.maf.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(last-split --version 2>&1 | sed 's/last-split //')
+ "${task.process}":
+ last: \$(last-split --version 2>&1 | sed 's/last-split //')
END_VERSIONS
"""
}
diff --git a/modules/last/train/functions.nf b/modules/last/train/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/last/train/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/last/train/main.nf b/modules/last/train/main.nf
index f0b958bc..0a949857 100644
--- a/modules/last/train/main.nf
+++ b/modules/last/train/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LAST_TRAIN {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::last=1250' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/last:1250--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0' :
+ 'quay.io/biocontainers/last:1250--h2e03b76_0' }"
input:
tuple val(meta), path(fastx)
@@ -27,20 +16,21 @@ process LAST_TRAIN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
last-train \\
- $options.args \\
+ $args \\
-P $task.cpus \\
${index}/\$INDEX_NAME \\
$fastx \\
> ${prefix}.\$INDEX_NAME.par
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(lastdb --version | sed 's/lastdb //')
+ "${task.process}":
+ last: \$(lastdb --version | sed 's/lastdb //')
END_VERSIONS
"""
}
diff --git a/modules/leehom/functions.nf b/modules/leehom/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/leehom/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/leehom/main.nf b/modules/leehom/main.nf
index e0d9ee39..d997e68b 100644
--- a/modules/leehom/main.nf
+++ b/modules/leehom/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION="1.2.15"
+def VERSION = '1.2.15' // Version information not provided by tool on CLI
process LEEHOM {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1"
- } else {
- container "quay.io/biocontainers/leehom:1.2.15--h29e30f7_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' :
+ 'quay.io/biocontainers/leehom:1.2.15--h29e30f7_1' }"
input:
tuple val(meta), path(reads)
@@ -32,54 +21,54 @@ process LEEHOM {
tuple val(meta), path("${prefix}_r2.fq.gz") , optional: true, emit: unmerged_r2_fq_pass
tuple val(meta), path("${prefix}_r2.fail.fq.gz"), optional: true, emit: unmerged_r2_fq_fail
tuple val(meta), path("*.log") , emit: log
-
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
- if ( reads.toString().endsWith('.bam') ) {
- """
- leeHom \\
- $options.args \\
- -t $task.cpus \\
- -o ${prefix}.bam \\
- --log ${prefix}.log \\
- $reads
+ if (reads.toString().endsWith('.bam')) {
+ """
+ leeHom \\
+ $args \\
+ -t $task.cpus \\
+ -o ${prefix}.bam \\
+ --log ${prefix}.log \\
+ $reads
- cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo $VERSION )
- END_VERSIONS
- """
- } else if ( meta.single_end ) {
- """
- leeHom \\
- $options.args \\
- -t $task.cpus \\
- -fq1 $reads \\
- -fqo ${prefix} \\
- --log ${prefix}.log
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ leehom: $VERSION
+ END_VERSIONS
+ """
+ } else if (meta.single_end) {
+ """
+ leeHom \\
+ $args \\
+ -t $task.cpus \\
+ -fq1 $reads \\
+ -fqo $prefix \\
+ --log ${prefix}.log
- cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo $VERSION )
- END_VERSIONS
- """
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ leehom: $VERSION
+ END_VERSIONS
+ """
} else {
- """
- leeHom \\
- $options.args \\
- -t $task.cpus \\
- -fq1 ${reads[0]} \\
- -fq2 ${reads[1]} \\
- -fqo ${prefix} \\
- --log ${prefix}.log
+ """
+ leeHom \\
+ $args \\
+ -t $task.cpus \\
+ -fq1 ${reads[0]} \\
+ -fq2 ${reads[1]} \\
+ -fqo $prefix \\
+ --log ${prefix}.log
- cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo $VERSION )
- END_VERSIONS
- """
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ leehom: $VERSION
+ END_VERSIONS
+ """
}
}
diff --git a/modules/lib/functions.nf b/modules/lib/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lib/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lima/functions.nf b/modules/lima/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lima/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lima/main.nf b/modules/lima/main.nf
index 16525953..64f6d87d 100644
--- a/modules/lima/main.nf
+++ b/modules/lima/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LIMA {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::lima=2.2.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0"
- } else {
- container "quay.io/biocontainers/lima:2.2.0--h9ee0642_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' :
+ 'quay.io/biocontainers/lima:2.2.0--h9ee0642_0' }"
input:
tuple val(meta), path(ccs)
@@ -40,7 +29,8 @@ process LIMA {
tuple val(meta), path("*.json") , optional: true, emit: json
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
OUT_EXT=""
@@ -62,11 +52,11 @@ process LIMA {
$primers \\
$prefix.\$OUT_EXT \\
-j $task.cpus \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' )
+ "${task.process}":
+ lima: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' )
END_VERSIONS
"""
}
diff --git a/modules/lissero/functions.nf b/modules/lissero/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lissero/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lissero/main.nf b/modules/lissero/main.nf
index ff863aaa..b5cd2b68 100644
--- a/modules/lissero/main.nf
+++ b/modules/lissero/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LISSERO {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::lissero=0.4.9" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0"
- } else {
- container "quay.io/biocontainers/lissero:0.4.9--py_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/lissero:0.4.9--py_0' :
+ 'quay.io/biocontainers/lissero:0.4.9--py_0' }"
input:
tuple val(meta), path(fasta)
@@ -26,16 +15,17 @@ process LISSERO {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
lissero \\
- $options.args \\
+ $args \\
$fasta \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(lissero --version 2>&1) | sed 's/^.*LisSero //' )
+ "${task.process}":
+ lissero: \$( echo \$(lissero --version 2>&1) | sed 's/^.*LisSero //' )
END_VERSIONS
"""
}
diff --git a/modules/lofreq/call/functions.nf b/modules/lofreq/call/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lofreq/call/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lofreq/call/main.nf b/modules/lofreq/call/main.nf
index e77d7a78..74995152 100644
--- a/modules/lofreq/call/main.nf
+++ b/modules/lofreq/call/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LOFREQ_CALL {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
- } else {
- container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
+ 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
input:
tuple val(meta), path(bam)
@@ -27,18 +16,19 @@ process LOFREQ_CALL {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
lofreq \\
call \\
- $options.args \\
+ $args \\
-f $fasta \\
-o ${prefix}.vcf.gz \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+ "${task.process}":
+ lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/lofreq/callparallel/functions.nf b/modules/lofreq/callparallel/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lofreq/callparallel/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf
index a86748d7..63ae2886 100644
--- a/modules/lofreq/callparallel/main.nf
+++ b/modules/lofreq/callparallel/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LOFREQ_CALLPARALLEL {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
- } else {
- container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
+ 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -28,19 +17,20 @@ process LOFREQ_CALLPARALLEL {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
lofreq \\
call-parallel \\
--pp-threads $task.cpus \\
- $options.args \\
+ $args \\
-f $fasta \\
-o ${prefix}.vcf.gz \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+ "${task.process}":
+ lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/lofreq/filter/functions.nf b/modules/lofreq/filter/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lofreq/filter/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lofreq/filter/main.nf b/modules/lofreq/filter/main.nf
index 905a961d..6f13ae44 100644
--- a/modules/lofreq/filter/main.nf
+++ b/modules/lofreq/filter/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LOFREQ_FILTER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
- } else {
- container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
+ 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
input:
tuple val(meta), path(vcf)
@@ -26,17 +15,18 @@ process LOFREQ_FILTER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
lofreq \\
filter \\
- $options.args \\
+ $args \\
-i $vcf \\
-o ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+ "${task.process}":
+ lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/lofreq/indelqual/functions.nf b/modules/lofreq/indelqual/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/lofreq/indelqual/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/lofreq/indelqual/main.nf b/modules/lofreq/indelqual/main.nf
index b33a1e04..bf04c5d2 100644
--- a/modules/lofreq/indelqual/main.nf
+++ b/modules/lofreq/indelqual/main.nf
@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process LOFREQ_INDELQUAL {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::lofreq=2.1.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
- } else {
- container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
+ 'quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
input:
tuple val(meta), path(bam)
@@ -26,17 +16,18 @@ process LOFREQ_INDELQUAL {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
lofreq indelqual \\
- $options.args \\
+ $args \\
-f $fasta \\
-o ${prefix}.bam \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+ "${task.process}":
+ lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/macs2/callpeak/functions.nf b/modules/macs2/callpeak/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/macs2/callpeak/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/macs2/callpeak/main.nf b/modules/macs2/callpeak/main.nf
index 94f8945b..e8bfcda0 100644
--- a/modules/macs2/callpeak/main.nf
+++ b/modules/macs2/callpeak/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MACS2_CALLPEAK {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3"
- } else {
- container "quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3' :
+ 'quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3' }"
input:
tuple val(meta), path(ipbam), path(controlbam)
@@ -32,20 +21,21 @@ process MACS2_CALLPEAK {
tuple val(meta), path("*.bdg") , optional:true, emit: bdg
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
- def args = options.args.tokenize()
- def format = meta.single_end ? 'BAM' : 'BAMPE'
- def control = controlbam ? "--control $controlbam" : ''
- if(args.contains('--format')){
- def id = args.findIndexOf{it=='--format'}
- format = args[id+1]
- args.remove(id+1)
- args.remove(id)
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def args_list = args.tokenize()
+ def format = meta.single_end ? 'BAM' : 'BAMPE'
+ def control = controlbam ? "--control $controlbam" : ''
+ if(args_list.contains('--format')){
+ def id = args_list.findIndexOf{it=='--format'}
+ format = args_list[id+1]
+ args_list.remove(id+1)
+ args_list.remove(id)
}
"""
macs2 \\
callpeak \\
- ${args.join(' ')} \\
+ ${args_list.join(' ')} \\
--gsize $macs2_gsize \\
--format $format \\
--name $prefix \\
@@ -53,8 +43,8 @@ process MACS2_CALLPEAK {
$control
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(macs2 --version | sed -e "s/macs2 //g")
+ "${task.process}":
+ macs2: \$(macs2 --version | sed -e "s/macs2 //g")
END_VERSIONS
"""
}
diff --git a/modules/malt/build/functions.nf b/modules/malt/build/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/malt/build/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/malt/build/main.nf b/modules/malt/build/main.nf
index 48259a50..d1b0c427 100644
--- a/modules/malt/build/main.nf
+++ b/modules/malt/build/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MALT_BUILD {
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/malt:0.53--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' :
+ 'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
input:
path fastas
@@ -30,6 +19,7 @@ process MALT_BUILD {
path "malt-build.log", emit: log
script:
+ def args = task.ext.args ?: ''
def avail_mem = 6
if (!task.memory) {
log.info '[MALT_BUILD] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@@ -46,13 +36,13 @@ process MALT_BUILD {
-s $seq_type \\
$igff \\
-d 'malt_index/' \\
- -t ${task.cpus} \\
- $options.args \\
+ -t $task.cpus \\
+ $args \\
-mdb ${map_db}/*.db |&tee malt-build.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2)
+ "${task.process}":
+ malt: \$(malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2)
END_VERSIONS
"""
}
diff --git a/modules/malt/run/functions.nf b/modules/malt/run/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/malt/run/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf
index bc78de8c..8b8f05cc 100644
--- a/modules/malt/run/main.nf
+++ b/modules/malt/run/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MALT_RUN {
label 'process_high_memory'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::malt=0.53" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/malt:0.53--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' :
+ 'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
input:
path fastqs
@@ -30,6 +19,7 @@ process MALT_RUN {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def avail_mem = 6
if (!task.memory) {
log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
@@ -40,17 +30,17 @@ process MALT_RUN {
"""
malt-run \\
-J-Xmx${avail_mem}g \\
- -t ${task.cpus} \\
+ -t $task.cpus \\
-v \\
-o . \\
- $options.args \\
+ $args \\
--inFile ${fastqs.join(' ')} \\
-m $mode \\
--index $index/ |&tee malt-run.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(malt-run --help 2>&1 | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ')
+ "${task.process}":
+ malt: \$(malt-run --help 2>&1 | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ')
END_VERSIONS
"""
}
diff --git a/modules/maltextract/functions.nf b/modules/maltextract/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/maltextract/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/maltextract/main.nf b/modules/maltextract/main.nf
index d909ec96..e3a42016 100644
--- a/modules/maltextract/main.nf
+++ b/modules/maltextract/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MALTEXTRACT {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::hops=0.35" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1"
- } else {
- container "quay.io/biocontainers/hops:0.35--hdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hops:0.35--hdfd78af_1' :
+ 'quay.io/biocontainers/hops:0.35--hdfd78af_1' }"
input:
path rma6
@@ -28,6 +17,7 @@ process MALTEXTRACT {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
MaltExtract \\
-Xmx${task.memory.toGiga()}g \\
@@ -36,11 +26,11 @@ process MALTEXTRACT {
-t $taxon_list \\
-r $ncbi_dir \\
-o results/ \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
+ "${task.process}":
+ maltextract: \$(MaltExtract --help | head -n 2 | tail -n 1 | sed 's/MaltExtract version//')
END_VERSIONS
"""
}
diff --git a/modules/manta/germline/functions.nf b/modules/manta/germline/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/manta/germline/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/manta/germline/main.nf b/modules/manta/germline/main.nf
index f957a7ec..553f0be9 100644
--- a/modules/manta/germline/main.nf
+++ b/modules/manta/germline/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MANTA_GERMLINE {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1"
- } else {
- container "quay.io/biocontainers/manta:1.6.0--h9ee0642_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' :
+ 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(input_index)
@@ -35,7 +24,8 @@ process MANTA_GERMLINE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
"""
configManta.py \
@@ -59,10 +49,9 @@ process MANTA_GERMLINE {
mv manta/results/variants/diploidSV.vcf.gz.tbi \
${prefix}.diploid_sv.vcf.gz.tbi
-
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( configManta.py --version )
+ "${task.process}":
+ manta: \$( configManta.py --version )
END_VERSIONS
"""
}
diff --git a/modules/manta/somatic/functions.nf b/modules/manta/somatic/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/manta/somatic/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/manta/somatic/main.nf b/modules/manta/somatic/main.nf
index f912d478..38d73133 100644
--- a/modules/manta/somatic/main.nf
+++ b/modules/manta/somatic/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MANTA_SOMATIC {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1"
- } else {
- container "quay.io/biocontainers/manta:1.6.0--h9ee0642_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' :
+ 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor)
@@ -37,7 +26,8 @@ process MANTA_SOMATIC {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
"""
@@ -60,8 +50,8 @@ process MANTA_SOMATIC {
mv manta/results/variants/somaticSV.vcf.gz.tbi ${prefix}.somatic_sv.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( configManta.py --version )
+ "${task.process}":
+ manta: \$( configManta.py --version )
END_VERSIONS
"""
}
diff --git a/modules/manta/tumoronly/functions.nf b/modules/manta/tumoronly/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/manta/tumoronly/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/manta/tumoronly/main.nf b/modules/manta/tumoronly/main.nf
index f20e8128..dc72fcc4 100644
--- a/modules/manta/tumoronly/main.nf
+++ b/modules/manta/tumoronly/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MANTA_TUMORONLY {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1"
- } else {
- container "quay.io/biocontainers/manta:1.6.0--h9ee0642_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' :
+ 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(input_index)
@@ -35,7 +24,8 @@ process MANTA_TUMORONLY {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def options_manta = target_bed ? "--exome --callRegions $target_bed" : ""
"""
configManta.py \
@@ -59,10 +49,9 @@ process MANTA_TUMORONLY {
mv manta/results/variants/tumorSV.vcf.gz.tbi \
${prefix}.tumor_sv.vcf.gz.tbi
-
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( configManta.py --version )
+ "${task.process}":
+ manta: \$( configManta.py --version )
END_VERSIONS
"""
}
diff --git a/modules/mapdamage2/functions.nf b/modules/mapdamage2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mapdamage2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mapdamage2/main.nf b/modules/mapdamage2/main.nf
index e252e27c..3673970e 100644
--- a/modules/mapdamage2/main.nf
+++ b/modules/mapdamage2/main.nf
@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MAPDAMAGE2 {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0"
- } else {
- container "quay.io/biocontainers/mapdamage2:2.2.1--pyr40_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mapdamage2:2.2.1--pyr40_0' :
+ 'quay.io/biocontainers/mapdamage2:2.2.1--pyr40_0' }"
input:
tuple val(meta), path(bam)
@@ -43,16 +33,17 @@ process MAPDAMAGE2 {
path "versions.yml",emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mapDamage \\
- $options.args \\
+ $args \\
-i $bam \\
-r $fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(mapDamage --version))
+ "${task.process}":
+ mapdamage2: \$(echo \$(mapDamage --version))
END_VERSIONS
"""
}
diff --git a/modules/mash/sketch/functions.nf b/modules/mash/sketch/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mash/sketch/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mash/sketch/main.nf b/modules/mash/sketch/main.nf
index f434a5f1..0c0b6e17 100644
--- a/modules/mash/sketch/main.nf
+++ b/modules/mash/sketch/main.nf
@@ -1,20 +1,10 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MASH_SKETCH {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mash=2.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1"
- } else {
- container "quay.io/biocontainers/mash:2.3--he348c14_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' :
+ 'quay.io/biocontainers/mash:2.3--he348c14_1' }"
input:
tuple val(meta), path(reads)
@@ -25,19 +15,20 @@ process MASH_SKETCH {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mash \\
sketch \\
- $options.args \\
+ $args \\
-p $task.cpus \\
-o ${prefix} \\
-r $reads \\
2> ${prefix}.mash_stats
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(mash --version 2>&1)
+ "${task.process}":
+ mash: \$(mash --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/mashtree/functions.nf b/modules/mashtree/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mashtree/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mashtree/main.nf b/modules/mashtree/main.nf
index db0b14f5..6728e3ce 100644
--- a/modules/mashtree/main.nf
+++ b/modules/mashtree/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MASHTREE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mashtree=1.2.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0"
- } else {
- container "quay.io/biocontainers/mashtree:1.2.0--pl526h516909a_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mashtree:1.2.0--pl526h516909a_0' :
+ 'quay.io/biocontainers/mashtree:1.2.0--pl526h516909a_0' }"
input:
tuple val(meta), path(seqs)
@@ -27,18 +16,19 @@ process MASHTREE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mashtree \\
- $options.args \\
+ $args \\
--numcpus $task.cpus \\
--outmatrix ${prefix}.tsv \\
--outtree ${prefix}.dnd \\
$seqs
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
+ "${task.process}":
+ mashtree: \$( echo \$( mashtree --version 2>&1 ) | sed 's/^.*Mashtree //' )
END_VERSIONS
"""
}
diff --git a/modules/maxbin2/functions.nf b/modules/maxbin2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/maxbin2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/maxbin2/main.nf b/modules/maxbin2/main.nf
index bcfa9590..e13af704 100644
--- a/modules/maxbin2/main.nf
+++ b/modules/maxbin2/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MAXBIN2 {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2"
- } else {
- container "quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' :
+ 'quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2' }"
input:
tuple val(meta), path(contigs), path(reads), path(abund)
@@ -33,20 +22,21 @@ process MAXBIN2 {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def associate_files = reads ? "-reads $reads" : "-abund $abund"
"""
run_MaxBin.pl \\
-contig $contigs \\
$associate_files \\
-thread $task.cpus \\
- $options.args \\
+ $args \\
-out $prefix
gzip *.fasta *.noclass *.tooshort *log *.marker
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
+ "${task.process}":
maxbin2: \$( run_MaxBin.pl -v | head -n 1 | sed 's/MaxBin //' )
END_VERSIONS
"""
diff --git a/modules/medaka/functions.nf b/modules/medaka/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/medaka/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/medaka/main.nf b/modules/medaka/main.nf
index a0db4150..e7a8b9cc 100644
--- a/modules/medaka/main.nf
+++ b/modules/medaka/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MEDAKA {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0"
- } else {
- container "quay.io/biocontainers/medaka:1.4.4--py38h130def0_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0' :
+ 'quay.io/biocontainers/medaka:1.4.4--py38h130def0_0' }"
input:
tuple val(meta), path(reads), path(assembly)
@@ -26,11 +15,12 @@ process MEDAKA {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
medaka_consensus \\
-t $task.cpus \\
- $options.args \\
+ $args \\
-i $reads \\
-d $assembly \\
-o ./
@@ -40,8 +30,8 @@ process MEDAKA {
gzip -n ${prefix}.fa
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( medaka --version 2>&1 | sed 's/medaka //g' )
+ "${task.process}":
+ medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' )
END_VERSIONS
"""
}
diff --git a/modules/megahit/functions.nf b/modules/megahit/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/megahit/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/megahit/main.nf b/modules/megahit/main.nf
index 8c8a5555..011fa7d3 100644
--- a/modules/megahit/main.nf
+++ b/modules/megahit/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MEGAHIT {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::megahit=1.2.9 conda-forge::pigz=2.6" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' :
+ 'quay.io/biocontainers/mulled-v2-0f92c152b180c7cd39d9b0e6822f8c89ccb59c99:8ec213d21e5d03f9db54898a2baeaf8ec729b447-0' }"
input:
tuple val(meta), path(reads)
@@ -30,25 +19,27 @@ process MEGAHIT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
megahit \\
-r ${reads} \\
-t $task.cpus \\
- $options.args \\
+ $args \\
--out-prefix $prefix
pigz \\
--no-name \\
-p $task.cpus \\
- $options.args2 \\
+ $args2 \\
megahit_out/*.fa \\
megahit_out/intermediate_contigs/*.fa
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
+ "${task.process}":
+ megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
END_VERSIONS
"""
} else {
@@ -57,19 +48,19 @@ process MEGAHIT {
-1 ${reads[0]} \\
-2 ${reads[1]} \\
-t $task.cpus \\
- $options.args \\
+ $args \\
--out-prefix $prefix
pigz \\
--no-name \\
-p $task.cpus \\
- $options.args2 \\
+ $args2 \\
megahit_out/*.fa \\
megahit_out/intermediate_contigs/*.fa
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
+ "${task.process}":
+ megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
END_VERSIONS
"""
}
diff --git a/modules/meningotype/functions.nf b/modules/meningotype/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/meningotype/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/meningotype/main.nf b/modules/meningotype/main.nf
index 4e779e8c..5dde5633 100644
--- a/modules/meningotype/main.nf
+++ b/modules/meningotype/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MENINGOTYPE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/meningotype:0.8.5--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0' :
+ 'quay.io/biocontainers/meningotype:0.8.5--pyhdfd78af_0' }"
input:
tuple val(meta), path(fasta)
@@ -26,16 +15,17 @@ process MENINGOTYPE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
meningotype \\
- $options.args \\
+ $args \\
$fasta \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(meningotype --version 2>&1) | sed 's/^.*meningotype v//' )
+ "${task.process}":
+ meningotype: \$( echo \$(meningotype --version 2>&1) | sed 's/^.*meningotype v//' )
END_VERSIONS
"""
}
diff --git a/modules/metabat2/jgisummarizebamcontigdepths/functions.nf b/modules/metabat2/jgisummarizebamcontigdepths/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/metabat2/jgisummarizebamcontigdepths/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/metabat2/jgisummarizebamcontigdepths/main.nf
index 1860ae16..e35d6715 100644
--- a/modules/metabat2/jgisummarizebamcontigdepths/main.nf
+++ b/modules/metabat2/jgisummarizebamcontigdepths/main.nf
@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::metabat2=2.15" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1"
- } else {
- container "quay.io/biocontainers/metabat2:2.15--h986a166_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' :
+ 'quay.io/biocontainers/metabat2:2.15--h986a166_1' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -25,20 +15,21 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
export OMP_NUM_THREADS=$task.cpus
jgi_summarize_bam_contig_depths \\
--outputDepth ${prefix}.txt \\
- $options.args \\
+ $args \\
$bam
bgzip --threads $task.cpus ${prefix}.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
+ "${task.process}":
+ metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
END_VERSIONS
"""
}
diff --git a/modules/metabat2/metabat2/functions.nf b/modules/metabat2/metabat2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/metabat2/metabat2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/metabat2/metabat2/main.nf b/modules/metabat2/metabat2/main.nf
index 589e268c..d158af91 100644
--- a/modules/metabat2/metabat2/main.nf
+++ b/modules/metabat2/metabat2/main.nf
@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process METABAT2_METABAT2 {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::metabat2=2.15" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1"
- } else {
- container "quay.io/biocontainers/metabat2:2.15--h986a166_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' :
+ 'quay.io/biocontainers/metabat2:2.15--h986a166_1' }"
input:
tuple val(meta), path(fasta), path(depth)
@@ -26,14 +16,15 @@ process METABAT2_METABAT2 {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def decompress_depth = depth ? "gzip -d -f $depth" : ""
def depth_file = depth ? "-a ${depth.baseName}" : ""
"""
$decompress_depth
metabat2 \\
- $options.args \\
+ $args \\
-i $fasta \\
$depth_file \\
-t $task.cpus \\
@@ -46,8 +37,8 @@ process METABAT2_METABAT2 {
bgzip --threads $task.cpus bins/*.fa
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
+ "${task.process}":
+ metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
END_VERSIONS
"""
}
diff --git a/modules/metaphlan3/functions.nf b/modules/metaphlan3/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/metaphlan3/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf
index c5157b66..9463da6f 100644
--- a/modules/metaphlan3/main.nf
+++ b/modules/metaphlan3/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process METAPHLAN3 {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::metaphlan=3.0.12' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0"
- } else {
- container "quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0' :
+ 'quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0' }"
input:
tuple val(meta), path(input)
@@ -29,7 +18,8 @@ process METAPHLAN3 {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def input_type = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" : ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
def input_data = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
@@ -39,14 +29,14 @@ process METAPHLAN3 {
--nproc $task.cpus \\
$input_type \\
$input_data \\
- $options.args \\
+ $args \\
$bowtie2_out \\
--bowtie2db ${metaphlan_db} \\
--biom ${prefix}.biom \\
--output_file ${prefix}_profile.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(metaphlan --version 2>&1 | awk '{print \$3}')
+ "${task.process}":
+ metaphlan3: \$(metaphlan --version 2>&1 | awk '{print \$3}')
END_VERSIONS
"""
}
diff --git a/modules/methyldackel/extract/functions.nf b/modules/methyldackel/extract/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/methyldackel/extract/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/methyldackel/extract/main.nf b/modules/methyldackel/extract/main.nf
index 94e4b379..a39c0305 100644
--- a/modules/methyldackel/extract/main.nf
+++ b/modules/methyldackel/extract/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process METHYLDACKEL_EXTRACT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
- } else {
- container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' :
+ 'quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -28,15 +17,16 @@ process METHYLDACKEL_EXTRACT {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
MethylDackel extract \\
- $options.args \\
+ $args \\
$fasta \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
+ "${task.process}":
+ methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
END_VERSIONS
"""
}
diff --git a/modules/methyldackel/mbias/functions.nf b/modules/methyldackel/mbias/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/methyldackel/mbias/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/methyldackel/mbias/main.nf b/modules/methyldackel/mbias/main.nf
index c8fd2fa2..1b4b14c4 100644
--- a/modules/methyldackel/mbias/main.nf
+++ b/modules/methyldackel/mbias/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process METHYLDACKEL_MBIAS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::methyldackel=0.6.0' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
- } else {
- container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0' :
+ 'quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -28,10 +17,11 @@ process METHYLDACKEL_MBIAS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
MethylDackel mbias \\
- $options.args \\
+ $args \\
$fasta \\
$bam \\
$prefix \\
@@ -39,8 +29,8 @@ process METHYLDACKEL_MBIAS {
> ${prefix}.mbias.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
+ "${task.process}":
+ methyldackel: \$(MethylDackel --version 2>&1 | cut -f1 -d" ")
END_VERSIONS
"""
}
diff --git a/modules/minia/functions.nf b/modules/minia/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/minia/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/minia/main.nf b/modules/minia/main.nf
index 140ef9e7..8516ef6e 100644
--- a/modules/minia/main.nf
+++ b/modules/minia/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MINIA {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::minia=3.2.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0"
- } else {
- container "quay.io/biocontainers/minia:3.2.4--he513fc3_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0' :
+ 'quay.io/biocontainers/minia:3.2.4--he513fc3_0' }"
input:
tuple val(meta), path(reads)
@@ -28,19 +17,20 @@ process MINIA {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def read_list = reads.join(",")
"""
echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt
minia \\
- $options.args \\
+ $args \\
-nb-cores $task.cpus \\
-in input_files.txt \\
-out $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
+ "${task.process}":
+ minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
END_VERSIONS
"""
}
diff --git a/modules/miniasm/functions.nf b/modules/miniasm/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/miniasm/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/miniasm/main.nf b/modules/miniasm/main.nf
index d2652fab..35c2e2c0 100644
--- a/modules/miniasm/main.nf
+++ b/modules/miniasm/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MINIASM {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::miniasm=0.3_r179" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2"
- } else {
- container "quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/miniasm:0.3_r179--h5bf99c6_2' :
+ 'quay.io/biocontainers/miniasm:0.3_r179--h5bf99c6_2' }"
input:
tuple val(meta), path(reads), path(paf)
@@ -27,10 +16,11 @@ process MINIASM {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
miniasm \\
- $options.args \\
+ $args \\
-f $reads \\
$paf > \\
${prefix}.gfa
@@ -41,8 +31,8 @@ process MINIASM {
gzip -n ${prefix}.fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( miniasm -V 2>&1 )
+ "${task.process}":
+ miniasm: \$( miniasm -V 2>&1 )
END_VERSIONS
"""
}
diff --git a/modules/minimap2/align/functions.nf b/modules/minimap2/align/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/minimap2/align/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index 215e4fb5..c6c0c316 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MINIMAP2_ALIGN {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
- } else {
- container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
+ 'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
input:
tuple val(meta), path(reads)
@@ -27,19 +16,20 @@ process MINIMAP2_ALIGN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
"""
minimap2 \\
- $options.args \\
+ $args \\
-t $task.cpus \\
$reference \\
$input_reads \\
> ${prefix}.paf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(minimap2 --version 2>&1)
+ "${task.process}":
+ minimap2: \$(minimap2 --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/minimap2/index/functions.nf b/modules/minimap2/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/minimap2/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/minimap2/index/main.nf b/modules/minimap2/index/main.nf
index b154a649..10cdd142 100644
--- a/modules/minimap2/index/main.nf
+++ b/modules/minimap2/index/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MINIMAP2_INDEX {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:['']) }
conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
- } else {
- container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
+ 'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
input:
path fasta
@@ -25,16 +14,17 @@ process MINIMAP2_INDEX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
minimap2 \\
-t $task.cpus \\
-d ${fasta.baseName}.mmi \\
- $options.args \\
+ $args \\
$fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(minimap2 --version 2>&1)
+ "${task.process}":
+ minimap2: \$(minimap2 --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/mlst/functions.nf b/modules/mlst/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mlst/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mlst/main.nf b/modules/mlst/main.nf
index faac9871..aa338420 100644
--- a/modules/mlst/main.nf
+++ b/modules/mlst/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MLST {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1"
- } else {
- container "quay.io/biocontainers/mlst:2.19.0--hdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' :
+ 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }"
input:
tuple val(meta), path(fasta)
@@ -26,7 +15,8 @@ process MLST {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mlst \\
--threads $task.cpus \\
@@ -34,8 +24,8 @@ process MLST {
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
+ "${task.process}":
+ mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
END_VERSIONS
"""
diff --git a/modules/mosdepth/functions.nf b/modules/mosdepth/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mosdepth/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf
index 8fe3cfee..b25e6a3d 100644
--- a/modules/mosdepth/main.nf
+++ b/modules/mosdepth/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MOSDEPTH {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0"
- } else {
- container "quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0' :
+ 'quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -34,17 +23,18 @@ process MOSDEPTH {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def interval = window_size ? "--by ${window_size}" : "--by ${bed}"
"""
mosdepth \\
$interval \\
- $options.args \\
+ $args \\
$prefix \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
+ "${task.process}":
+ mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/msisensor/msi/functions.nf b/modules/msisensor/msi/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/msisensor/msi/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/msisensor/msi/main.nf b/modules/msisensor/msi/main.nf
index bd5a0a0e..1eb510a1 100644
--- a/modules/msisensor/msi/main.nf
+++ b/modules/msisensor/msi/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MSISENSOR_MSI {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
- } else {
- container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' :
+ 'quay.io/biocontainers/msisensor:0.5--hb3646a4_2' }"
input:
tuple val(meta), path(normal_bam), path(normal_bai), path(tumor_bam), path(tumor_bai), val(metascan), path(homopolymers)
@@ -29,7 +18,8 @@ process MSISENSOR_MSI {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
msisensor \\
msi \\
@@ -37,11 +27,11 @@ process MSISENSOR_MSI {
-n $normal_bam \\
-t $tumor_bam \\
-o $prefix \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
+ "${task.process}":
+ msisensor: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
END_VERSIONS
"""
}
diff --git a/modules/msisensor/scan/functions.nf b/modules/msisensor/scan/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/msisensor/scan/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/msisensor/scan/main.nf b/modules/msisensor/scan/main.nf
index ebd8785a..2419a0a1 100644
--- a/modules/msisensor/scan/main.nf
+++ b/modules/msisensor/scan/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MSISENSOR_SCAN {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::msisensor=0.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2"
- } else {
- container "quay.io/biocontainers/msisensor:0.5--hb3646a4_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/msisensor:0.5--hb3646a4_2' :
+ 'quay.io/biocontainers/msisensor:0.5--hb3646a4_2' }"
input:
tuple val(meta), path(fasta)
@@ -26,17 +15,18 @@ process MSISENSOR_SCAN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
msisensor \\
scan \\
-d $fasta \\
-o ${prefix}.msisensor_scan.tab \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
+ "${task.process}":
+ msisensor: \$(msisensor 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p')
END_VERSIONS
"""
}
diff --git a/modules/mtnucratio/functions.nf b/modules/mtnucratio/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mtnucratio/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mtnucratio/main.nf b/modules/mtnucratio/main.nf
index 28d08a13..b8663469 100644
--- a/modules/mtnucratio/main.nf
+++ b/modules/mtnucratio/main.nf
@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MTNUCRATIO {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2"
- } else {
- container "quay.io/biocontainers/mtnucratio:0.7--hdfd78af_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mtnucratio:0.7--hdfd78af_2' :
+ 'quay.io/biocontainers/mtnucratio:0.7--hdfd78af_2' }"
input:
tuple val(meta), path(bam)
@@ -27,17 +17,18 @@ process MTNUCRATIO {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mtnucratio \\
- $options.args \\
+ $args \\
$bam \\
$mt_id
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(mtnucratio --version 2>&1) | head -n1 | sed 's/Version: //')
+ "${task.process}":
+ mtnucratio: \$(echo \$(mtnucratio --version 2>&1) | head -n1 | sed 's/Version: //')
END_VERSIONS
"""
}
diff --git a/modules/multiqc/functions.nf b/modules/multiqc/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/multiqc/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index 0861aa59..3dceb162 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MULTIQC {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
input:
path multiqc_files
@@ -27,12 +16,13 @@ process MULTIQC {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
- multiqc -f $options.args .
+ multiqc -f $args .
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+ "${task.process}":
+ multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
}
diff --git a/modules/mummer/functions.nf b/modules/mummer/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/mummer/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/mummer/main.nf b/modules/mummer/main.nf
index e46fd799..f4f3bb18 100644
--- a/modules/mummer/main.nf
+++ b/modules/mummer/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '3.23'
+def VERSION = '3.23' // Version information not provided by tool on CLI
process MUMMER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12"
- } else {
- container "quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' :
+ 'quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12' }"
input:
tuple val(meta), path(ref), path(query)
@@ -28,7 +17,8 @@ process MUMMER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false
def fasta_name_ref = ref.getName().replace(".gz", "")
@@ -42,14 +32,14 @@ process MUMMER {
gzip -c -d $query > $fasta_name_query
fi
mummer \\
- $options.args \\
+ $args \\
$fasta_name_ref \\
$fasta_name_query \\
> ${prefix}.coords
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo $VERSION )
+ "${task.process}":
+ mummer: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/muscle/functions.nf b/modules/muscle/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/muscle/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/muscle/main.nf b/modules/muscle/main.nf
index 6ffb97ac..a50f5cb3 100644
--- a/modules/muscle/main.nf
+++ b/modules/muscle/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process MUSCLE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6"
- } else {
- container "quay.io/biocontainers/muscle:3.8.1551--h7d875b9_6"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' :
+ 'quay.io/biocontainers/muscle:3.8.1551--h7d875b9_6' }"
input:
tuple val(meta), path(fasta)
@@ -33,18 +22,18 @@ process MUSCLE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
- def fasta_out = options.args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : ''
- def clw_out = options.args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : ''
- def msf_out = options.args.contains('-msf') ? "-msfout ${prefix}_muscle_msa.msf" : ''
- def phys_out = options.args.contains('-phys') ? "-physout ${prefix}_muscle_msa.phys" : ''
- def phyi_out = options.args.contains('-phyi') ? "-phyiout ${prefix}_muscle_msa.phyi" : ''
- def html_out = options.args.contains('-html') ? "-htmlout ${prefix}_muscle_msa.html" : ''
- def tree_out = options.args.contains('-maketree') ? "-out ${prefix}_muscle_msa.tree" : ''
-
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def fasta_out = args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : ''
+ def clw_out = args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : ''
+ def msf_out = args.contains('-msf') ? "-msfout ${prefix}_muscle_msa.msf" : ''
+ def phys_out = args.contains('-phys') ? "-physout ${prefix}_muscle_msa.phys" : ''
+ def phyi_out = args.contains('-phyi') ? "-phyiout ${prefix}_muscle_msa.phyi" : ''
+ def html_out = args.contains('-html') ? "-htmlout ${prefix}_muscle_msa.html" : ''
+ def tree_out = args.contains('-maketree') ? "-out ${prefix}_muscle_msa.tree" : ''
"""
muscle \\
- $options.args \\
+ $args \\
-in $fasta \\
$fasta_out \\
$clw_out \\
@@ -55,8 +44,8 @@ process MUSCLE {
$tree_out \\
-loga muscle_msa.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(muscle -version | sed 's/^MUSCLE v//; s/by.*\$//')
+ "${task.process}":
+ muscle: \$(muscle -version | sed 's/^MUSCLE v//; s/by.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/nanolyse/functions.nf b/modules/nanolyse/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/nanolyse/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/nanolyse/main.nf b/modules/nanolyse/main.nf
index 271592f7..f29eeb77 100644
--- a/modules/nanolyse/main.nf
+++ b/modules/nanolyse/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process NANOLYSE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::nanolyse=1.2.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0"
- } else {
- container "quay.io/biocontainers/nanolyse:1.2.0--py_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/nanolyse:1.2.0--py_0' :
+ 'quay.io/biocontainers/nanolyse:1.2.0--py_0' }"
input:
tuple val(meta), path(fastq)
@@ -28,14 +17,15 @@ process NANOLYSE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
gunzip -c $fastq | NanoLyse -r $fasta | gzip > ${prefix}.fastq.gz
mv NanoLyse.log ${prefix}.nanolyse.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(NanoLyse --version 2>&1 | sed -e "s/NanoLyse //g")
+ "${task.process}":
+ nanolyse: \$(NanoLyse --version 2>&1 | sed -e "s/NanoLyse //g")
END_VERSIONS
"""
}
diff --git a/modules/nanoplot/functions.nf b/modules/nanoplot/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/nanoplot/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf
index 16e2248c..36577d8a 100644
--- a/modules/nanoplot/main.nf
+++ b/modules/nanoplot/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process NANOPLOT {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0' :
+ 'quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0' }"
input:
tuple val(meta), path(ontfile)
@@ -29,16 +18,17 @@ process NANOPLOT {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
"""
NanoPlot \\
- $options.args \\
+ $args \\
-t $task.cpus \\
$input_file
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
+ "${task.process}":
+ nanoplot: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/ncbigenomedownload/functions.nf b/modules/ncbigenomedownload/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ncbigenomedownload/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ncbigenomedownload/main.nf b/modules/ncbigenomedownload/main.nf
index ffa53871..466c8d09 100644
--- a/modules/ncbigenomedownload/main.nf
+++ b/modules/ncbigenomedownload/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process NCBIGENOMEDOWNLOAD {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ncbi-genome-download=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.0--pyh864c0ab_1"
- } else {
- container "quay.io/biocontainers/ncbi-genome-download:0.3.0--pyh864c0ab_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ncbi-genome-download:0.3.0--pyh864c0ab_1' :
+ 'quay.io/biocontainers/ncbi-genome-download:0.3.0--pyh864c0ab_1' }"
input:
val meta
@@ -39,18 +28,19 @@ process NCBIGENOMEDOWNLOAD {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def accessions_opt = accessions ? "-A ${accessions}" : ""
"""
ncbi-genome-download \\
- $options.args \\
+ $args \\
$accessions_opt \\
--output-folder ./ \\
--flat-output
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( ncbi-genome-download --version )
+ "${task.process}":
+ ncbigenomedownload: \$( ncbi-genome-download --version )
END_VERSIONS
"""
}
diff --git a/modules/nextclade/functions.nf b/modules/nextclade/functions.nf
deleted file mode 100755
index 85628ee0..00000000
--- a/modules/nextclade/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/nextclade/main.nf b/modules/nextclade/main.nf
index 6fc6efc4..317d393d 100755
--- a/modules/nextclade/main.nf
+++ b/modules/nextclade/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process NEXTCLADE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::nextclade_js=0.14.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0"
- } else {
- container "quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0' :
+ 'quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0' }"
input:
tuple val(meta), path(fasta)
@@ -30,10 +19,11 @@ process NEXTCLADE {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
nextclade \\
- $options.args \\
+ $args \\
--jobs $task.cpus \\
--input-fasta $fasta \\
--output-json ${prefix}.json \\
@@ -43,8 +33,8 @@ process NEXTCLADE {
--output-tree ${prefix}.tree.json
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(nextclade --version 2>&1)
+ "${task.process}":
+ nextclade: \$(nextclade --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/ngmaster/functions.nf b/modules/ngmaster/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ngmaster/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ngmaster/main.nf b/modules/ngmaster/main.nf
index 1897b5f3..0884b55c 100644
--- a/modules/ngmaster/main.nf
+++ b/modules/ngmaster/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process NGMASTER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ngmaster=0.5.8" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1"
- } else {
- container "quay.io/biocontainers/ngmaster:0.5.8--pyhdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ngmaster:0.5.8--pyhdfd78af_1' :
+ 'quay.io/biocontainers/ngmaster:0.5.8--pyhdfd78af_1' }"
input:
tuple val(meta), path(fasta)
@@ -26,16 +15,17 @@ process NGMASTER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
ngmaster \\
- $options.args \\
+ $args \\
$fasta \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(ngmaster --version 2>&1) | sed 's/^.*ngmaster //' )
+ "${task.process}":
+ ngmaster: \$( echo \$(ngmaster --version 2>&1) | sed 's/^.*ngmaster //' )
END_VERSIONS
"""
}
diff --git a/modules/nucmer/functions.nf b/modules/nucmer/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/nucmer/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/nucmer/main.nf b/modules/nucmer/main.nf
index 49a275f4..bb5dcb7d 100644
--- a/modules/nucmer/main.nf
+++ b/modules/nucmer/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process NUCMER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12"
- } else {
- container "quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' :
+ 'quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12' }"
input:
tuple val(meta), path(ref), path(query)
@@ -27,7 +16,8 @@ process NUCMER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false
def is_compressed_query = query.getName().endsWith(".gz") ? true : false
def fasta_name_ref = ref.getName().replace(".gz", "")
@@ -43,13 +33,13 @@ process NUCMER {
nucmer \\
-p $prefix \\
--coords \\
- $options.args \\
+ $args \\
$fasta_name_ref \\
$fasta_name_query
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( nucmer --version 2>&1 | grep "version" | sed -e "s/NUCmer (NUCleotide MUMmer) version //g; s/nucmer//g;" )
+ "${task.process}":
+ nucmer: \$( nucmer --version 2>&1 | grep "version" | sed -e "s/NUCmer (NUCleotide MUMmer) version //g; s/nucmer//g;" )
END_VERSIONS
"""
}
diff --git a/modules/optitype/functions.nf b/modules/optitype/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/optitype/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/optitype/main.nf b/modules/optitype/main.nf
index 083b03a7..24be66a7 100644
--- a/modules/optitype/main.nf
+++ b/modules/optitype/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process OPTITYPE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::optitype=1.3.5" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/optitype:1.3.5--0"
- } else {
- container "quay.io/biocontainers/optitype:1.3.5--0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/optitype:1.3.5--0' :
+ 'quay.io/biocontainers/optitype:1.3.5--0' }"
input:
tuple val(meta), path(bam)
@@ -26,30 +15,32 @@ process OPTITYPE {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- # Create a config for OptiType on a per sample basis with options.args2
+ # Create a config for OptiType on a per sample basis with task.ext.args2
#Doing it old school now
echo "[mapping]" > config.ini
echo "razers3=razers3" >> config.ini
echo "threads=$task.cpus" >> config.ini
echo "[ilp]" >> config.ini
- echo "$options.args2" >> config.ini
+ echo "$args2" >> config.ini
echo "threads=1" >> config.ini
echo "[behavior]" >> config.ini
echo "deletebam=true" >> config.ini
echo "unpaired_weight=0" >> config.ini
echo "use_discordant=false" >> config.ini
- # Run the actual OptiType typing with options.args
- OptiTypePipeline.py -i ${bam} -c config.ini --${meta.seq_type} $options.args --prefix $prefix --outdir $prefix
+ # Run the actual OptiType typing with args
+ OptiTypePipeline.py -i ${bam} -c config.ini --${meta.seq_type} $args --prefix $prefix --outdir $prefix
#Couldn't find a nicer way of doing this
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g")
+ "${task.process}":
+ optitype: \$(cat \$(which OptiTypePipeline.py) | grep -e "Version:" | sed -e "s/Version: //g")
END_VERSIONS
"""
}
diff --git a/modules/pairix/functions.nf b/modules/pairix/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairix/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairix/main.nf b/modules/pairix/main.nf
index 4bfd3b0d..c1b9658c 100644
--- a/modules/pairix/main.nf
+++ b/modules/pairix/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRIX {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3"
- } else {
- container "quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
+ 'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
input:
tuple val(meta), path(pair)
@@ -26,14 +15,15 @@ process PAIRIX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
pairix \\
- $options.args \\
+ $args \\
$pair
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
+ "${task.process}":
+ pairix: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/pairtools/dedup/functions.nf b/modules/pairtools/dedup/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairtools/dedup/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairtools/dedup/main.nf b/modules/pairtools/dedup/main.nf
index eabf24dd..5ee9dc43 100644
--- a/modules/pairtools/dedup/main.nf
+++ b/modules/pairtools/dedup/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRTOOLS_DEDUP {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
- } else {
- container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
+ 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(input)
@@ -27,17 +16,18 @@ process PAIRTOOLS_DEDUP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pairtools dedup \\
- $options.args \\
+ $args \\
-o ${prefix}.pairs.gz \\
--output-stats ${prefix}.pairs.stat \\
$input
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
+ "${task.process}":
+ pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}
diff --git a/modules/pairtools/flip/functions.nf b/modules/pairtools/flip/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairtools/flip/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairtools/flip/main.nf b/modules/pairtools/flip/main.nf
index 50cfdfd2..452800cc 100644
--- a/modules/pairtools/flip/main.nf
+++ b/modules/pairtools/flip/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRTOOLS_FLIP {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
- } else {
- container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
+ 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(sam)
@@ -27,18 +16,19 @@ process PAIRTOOLS_FLIP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pairtools \\
flip \\
-c $chromsizes \\
- $options.args \\
+ $args \\
-o ${prefix}.flip.gz \\
$sam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
+ "${task.process}":
+ pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}
diff --git a/modules/pairtools/parse/functions.nf b/modules/pairtools/parse/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairtools/parse/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairtools/parse/main.nf b/modules/pairtools/parse/main.nf
index cd6099e1..1d34d42c 100644
--- a/modules/pairtools/parse/main.nf
+++ b/modules/pairtools/parse/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRTOOLS_PARSE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
- } else {
- container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
+ 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(bam)
@@ -28,19 +17,20 @@ process PAIRTOOLS_PARSE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pairtools \\
parse \\
-c $chromsizes \\
- $options.args \\
+ $args \\
--output-stats ${prefix}.pairsam.stat \\
-o ${prefix}.pairsam.gz \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
+ "${task.process}":
+ pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}
diff --git a/modules/pairtools/restrict/functions.nf b/modules/pairtools/restrict/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairtools/restrict/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairtools/restrict/main.nf b/modules/pairtools/restrict/main.nf
index b1b21da7..9fcc245c 100644
--- a/modules/pairtools/restrict/main.nf
+++ b/modules/pairtools/restrict/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRTOOLS_RESTRICT {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
- } else {
- container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
+ 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(pairs)
@@ -27,18 +16,19 @@ process PAIRTOOLS_RESTRICT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pairtools \\
restrict \\
-f $frag \\
- $options.args \\
+ $args \\
-o ${prefix}.pairs.gz \\
$pairs
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
+ "${task.process}":
+ pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}
diff --git a/modules/pairtools/select/functions.nf b/modules/pairtools/select/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairtools/select/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairtools/select/main.nf b/modules/pairtools/select/main.nf
index dec29573..f699afa3 100644
--- a/modules/pairtools/select/main.nf
+++ b/modules/pairtools/select/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRTOOLS_SELECT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
- } else {
- container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
+ 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(input)
@@ -27,17 +16,18 @@ process PAIRTOOLS_SELECT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pairtools select \\
- "$options.args" \\
+ "$args" \\
-o ${prefix}.selected.pairs.gz \\
--output-rest ${prefix}.unselected.pairs.gz \\
${input}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
+ "${task.process}":
+ pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}
diff --git a/modules/pairtools/sort/functions.nf b/modules/pairtools/sort/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pairtools/sort/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pairtools/sort/main.nf b/modules/pairtools/sort/main.nf
index 996bcb0b..5caa5b74 100644
--- a/modules/pairtools/sort/main.nf
+++ b/modules/pairtools/sort/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PAIRTOOLS_SORT {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
- } else {
- container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
+ 'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
input:
tuple val(meta), path(input)
@@ -26,20 +15,21 @@ process PAIRTOOLS_SORT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def mem = task.memory.toString().replaceAll(/(\s|\.|B)+/, '')
"""
pairtools \\
sort \\
- $options.args \\
+ $args \\
--nproc $task.cpus \\
--memory "$mem" \\
-o ${prefix}.pairs.gz \\
$input
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
+ "${task.process}":
+ pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
END_VERSIONS
"""
}
diff --git a/modules/pangolin/functions.nf b/modules/pangolin/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pangolin/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf
index edf67dd7..99a68e09 100644
--- a/modules/pangolin/main.nf
+++ b/modules/pangolin/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PANGOLIN {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::pangolin=3.1.11' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1'
- } else {
- container 'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1' :
+ 'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1' }"
input:
tuple val(meta), path(fasta)
@@ -26,17 +15,18 @@ process PANGOLIN {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pangolin \\
$fasta\\
--outfile ${prefix}.pangolin.csv \\
--threads $task.cpus \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pangolin --version | sed "s/pangolin //g")
+ "${task.process}":
+ pangolin: \$(pangolin --version | sed "s/pangolin //g")
END_VERSIONS
"""
}
diff --git a/modules/paraclu/functions.nf b/modules/paraclu/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/paraclu/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/paraclu/main.nf b/modules/paraclu/main.nf
index 6d65a784..a2003834 100644
--- a/modules/paraclu/main.nf
+++ b/modules/paraclu/main.nf
@@ -1,22 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
+def VERSION = '10' // Version information not provided by tool on CLI
process PARACLU {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::paraclu=10" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1"
- } else {
- container "quay.io/biocontainers/paraclu:10--h9a82719_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1' :
+ 'quay.io/biocontainers/paraclu:10--h9a82719_1' }"
input:
tuple val(meta), path(bed)
@@ -27,8 +18,8 @@ process PARACLU {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
- def VERSION=10
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
awk -F "\t" '{print\$1"\t"\$6"\t"\$2"\t"\$5}' < $bed > ${bed}_4P
@@ -38,8 +29,8 @@ process PARACLU {
awk -F '\t' '{print \$1"\t"\$3"\t"\$4"\t"\$1":"\$3".."\$4","\$2"\t"\$6"\t"\$2}' ${prefix}.clustered.simplified > ${prefix}.clustered.simplified.bed
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: $VERSION
+ "${task.process}":
+ paraclu: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/pbbam/pbmerge/functions.nf b/modules/pbbam/pbmerge/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pbbam/pbmerge/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pbbam/pbmerge/main.nf b/modules/pbbam/pbmerge/main.nf
index 63cd2ffe..970128cb 100644
--- a/modules/pbbam/pbmerge/main.nf
+++ b/modules/pbbam/pbmerge/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PBBAM_PBMERGE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1"
- } else {
- container "quay.io/biocontainers/pbbam:1.7.0--h058f120_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' :
+ 'quay.io/biocontainers/pbbam:1.7.0--h058f120_1' }"
input:
tuple val(meta), path(bam)
@@ -27,16 +16,17 @@ process PBBAM_PBMERGE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pbmerge \\
-o ${prefix}.bam \\
- $options.args \\
+ $args \\
*.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- pbbam/pbmerge: \$( pbmerge --version|sed 's/pbmerge //' )
+ "${task.process}":
+ pbbam: \$( pbmerge --version|sed 's/pbmerge //' )
END_VERSIONS
"""
}
diff --git a/modules/pbccs/functions.nf b/modules/pbccs/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pbccs/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf
index 55eacd76..83e56d96 100644
--- a/modules/pbccs/main.nf
+++ b/modules/pbccs/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PBCCS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0"
- } else {
- container "quay.io/biocontainers/pbccs:6.2.0--h9ee0642_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' :
+ 'quay.io/biocontainers/pbccs:6.2.0--h9ee0642_0' }"
input:
tuple val(meta), path(bam), path(pbi)
@@ -32,7 +21,8 @@ process PBCCS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
ccs \\
$bam \\
@@ -42,11 +32,11 @@ process PBCCS {
--metrics-json ${prefix}.chunk${chunk_num}.metrics.json.gz \\
--chunk $chunk_num/$chunk_on \\
-j $task.cpus \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
+ "${task.process}":
+ pbccs: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/peddy/functions.nf b/modules/peddy/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/peddy/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/peddy/main.nf b/modules/peddy/main.nf
index 4331ed9d..0a6c3384 100644
--- a/modules/peddy/main.nf
+++ b/modules/peddy/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PEDDY {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::peddy=0.4.8" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0"
- } else {
- container "quay.io/biocontainers/peddy:0.4.8--pyh5e36f6f_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/peddy:0.4.8--pyh5e36f6f_0' :
+ 'quay.io/biocontainers/peddy:0.4.8--pyh5e36f6f_0' }"
input:
tuple val(meta), path(vcf), path(vcf_tbi)
@@ -30,18 +19,19 @@ process PEDDY {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
peddy \\
- $options.args \\
+ $args \\
--plot \\
-p $task.cpus \\
$vcf \\
$ped
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
+ "${task.process}":
+ peddy: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
END_VERSIONS
"""
}
diff --git a/modules/phantompeakqualtools/functions.nf b/modules/phantompeakqualtools/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/phantompeakqualtools/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf
index b390bf7e..f2edabc3 100644
--- a/modules/phantompeakqualtools/main.nf
+++ b/modules/phantompeakqualtools/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '1.2.2'
+def VERSION = '1.2.2' // Version information not provided by tool on CLI
process PHANTOMPEAKQUALTOOLS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0"
- } else {
- container "quay.io/biocontainers/phantompeakqualtools:1.2.2--0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' :
+ 'quay.io/biocontainers/phantompeakqualtools:1.2.2--0' }"
input:
tuple val(meta), path(bam)
@@ -30,13 +19,15 @@ process PHANTOMPEAKQUALTOOLS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
RUN_SPP=`which run_spp.R`
Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
+
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ phantompeakqualtools: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/phyloflash/functions.nf b/modules/phyloflash/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/phyloflash/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/phyloflash/main.nf b/modules/phyloflash/main.nf
index 894c16a2..c507dd14 100644
--- a/modules/phyloflash/main.nf
+++ b/modules/phyloflash/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PHYLOFLASH {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::phyloflash=3.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1"
- } else {
- container "quay.io/biocontainers/phyloflash:3.4--hdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/phyloflash:3.4--hdfd78af_1' :
+ 'quay.io/biocontainers/phyloflash:3.4--hdfd78af_1' }"
input:
tuple val(meta), path(reads)
@@ -28,12 +17,12 @@ process PHYLOFLASH {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
phyloFlash.pl \\
- $options.args \\
+ $args \\
-read1 ${reads[0]} \\
-lib $prefix \\
-interleaved \\
@@ -44,14 +33,14 @@ process PHYLOFLASH {
mv ${prefix}.* $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
+ "${task.process}":
+ phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
END_VERSIONS
"""
} else {
"""
phyloFlash.pl \\
- $options.args \\
+ $args \\
-read1 ${reads[0]} \\
-read2 ${reads[1]} \\
-lib $prefix \\
@@ -62,24 +51,22 @@ process PHYLOFLASH {
mv ${prefix}.* $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
+ "${task.process}":
+ phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
END_VERSIONS
"""
}
stub:
-
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
mkdir ${prefix}
touch ${prefix}/${prefix}.SSU.collection.fasta
touch ${prefix}/${prefix}.phyloFlash
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
+ "${task.process}":
+ phyloflash: \$(echo \$(phyloFlash.pl -version 2>&1) | sed "s/^.*phyloFlash v//")
END_VERSIONS
"""
}
diff --git a/modules/picard/collecthsmetrics/functions.nf b/modules/picard/collecthsmetrics/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/collecthsmetrics/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index 1f7ad8e6..adb82d8c 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_COLLECTHSMETRICS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::picard=2.26.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.26.2--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.26.2--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.26.2--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.26.2--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -30,7 +19,8 @@ process PICARD_COLLECTHSMETRICS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def reference = fasta ? "-R $fasta" : ""
def avail_mem = 3
@@ -43,7 +33,7 @@ process PICARD_COLLECTHSMETRICS {
picard \\
-Xmx${avail_mem}g \\
CollectHsMetrics \\
- $options.args \\
+ $args \\
$reference \\
-BAIT_INTERVALS $bait_intervals \\
-TARGET_INTERVALS $target_intervals \\
@@ -51,8 +41,8 @@ process PICARD_COLLECTHSMETRICS {
-OUTPUT ${prefix}_collecthsmetrics.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/picard/collectmultiplemetrics/functions.nf b/modules/picard/collectmultiplemetrics/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/collectmultiplemetrics/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index dd8fdaca..f52f5885 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_COLLECTMULTIPLEMETRICS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -28,7 +17,8 @@ process PICARD_COLLECTMULTIPLEMETRICS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -39,14 +29,14 @@ process PICARD_COLLECTMULTIPLEMETRICS {
picard \\
-Xmx${avail_mem}g \\
CollectMultipleMetrics \\
- $options.args \\
+ $args \\
INPUT=$bam \\
OUTPUT=${prefix}.CollectMultipleMetrics \\
REFERENCE_SEQUENCE=$fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/picard/collectwgsmetrics/functions.nf b/modules/picard/collectwgsmetrics/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/collectwgsmetrics/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index 6028feef..94745d2d 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_COLLECTWGSMETRICS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -27,7 +16,8 @@ process PICARD_COLLECTWGSMETRICS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -38,14 +28,14 @@ process PICARD_COLLECTWGSMETRICS {
picard \\
-Xmx${avail_mem}g \\
CollectWgsMetrics \\
- $options.args \\
+ $args \\
INPUT=$bam \\
OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
REFERENCE_SEQUENCE=$fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/picard/filtersamreads/functions.nf b/modules/picard/filtersamreads/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/filtersamreads/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf
index 68cee34d..8b1d2e6b 100644
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_FILTERSAMREADS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(readlist)
@@ -27,7 +16,8 @@ process PICARD_FILTERSAMREADS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard FilterSamReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -42,11 +32,11 @@ process PICARD_FILTERSAMREADS {
--INPUT $bam \\
--OUTPUT ${prefix}.bam \\
--FILTER $filter \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} else if ( filter == 'includeReadList' || filter == 'excludeReadList' ) {
@@ -58,11 +48,11 @@ process PICARD_FILTERSAMREADS {
--OUTPUT ${prefix}.bam \\
--FILTER $filter \\
--READ_LIST_FILE $readlist \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/picard/markduplicates/functions.nf b/modules/picard/markduplicates/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/markduplicates/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index 130a1e52..d4c5886f 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_MARKDUPLICATES {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -28,7 +17,8 @@ process PICARD_MARKDUPLICATES {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -39,14 +29,14 @@ process PICARD_MARKDUPLICATES {
picard \\
-Xmx${avail_mem}g \\
MarkDuplicates \\
- $options.args \\
+ $args \\
I=$bam \\
O=${prefix}.bam \\
M=${prefix}.MarkDuplicates.metrics.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/picard/mergesamfiles/functions.nf b/modules/picard/mergesamfiles/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/mergesamfiles/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index 355c0bf3..3a2fc620 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_MERGESAMFILES {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
input:
tuple val(meta), path(bams)
@@ -26,7 +15,8 @@ process PICARD_MERGESAMFILES {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def bam_files = bams.sort()
def avail_mem = 3
if (!task.memory) {
@@ -39,20 +29,20 @@ process PICARD_MERGESAMFILES {
picard \\
-Xmx${avail_mem}g \\
MergeSamFiles \\
- $options.args \\
+ $args \\
${'INPUT='+bam_files.join(' INPUT=')} \\
OUTPUT=${prefix}.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
} else {
"""
ln -s ${bam_files[0]} ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/picard/sortsam/functions.nf b/modules/picard/sortsam/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/picard/sortsam/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf
index 939df1c0..b264b927 100644
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@@ -1,23 +1,11 @@
-
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PICARD_SORTSAM {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0' :
+ 'quay.io/biocontainers/picard:2.25.7--hdfd78af_0' }"
input:
tuple val(meta), path(bam)
@@ -28,7 +16,8 @@ process PICARD_SORTSAM {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def avail_mem = 3
if (!task.memory) {
log.info '[Picard SortSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -44,8 +33,8 @@ process PICARD_SORTSAM {
--SORT_ORDER $sort_order
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(picard SortSam --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+ "${task.process}":
+ picard: \$(picard SortSam --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
}
diff --git a/modules/pirate/functions.nf b/modules/pirate/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pirate/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pirate/main.nf b/modules/pirate/main.nf
index 01a950dd..3bbb1d64 100644
--- a/modules/pirate/main.nf
+++ b/modules/pirate/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PIRATE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1"
- } else {
- container "quay.io/biocontainers/pirate:1.0.4--hdfd78af_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1' :
+ 'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }"
input:
tuple val(meta), path(gff)
@@ -27,17 +16,18 @@ process PIRATE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
PIRATE \\
- $options.args \\
+ $args \\
--threads $task.cpus \\
--input ./ \\
--output results/
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
+ "${task.process}":
+ pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
END_VERSIONS
"""
}
diff --git a/modules/plasmidid/functions.nf b/modules/plasmidid/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/plasmidid/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/plasmidid/main.nf b/modules/plasmidid/main.nf
index 1edc5eeb..290ae549 100644
--- a/modules/plasmidid/main.nf
+++ b/modules/plasmidid/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PLASMIDID {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::plasmidid=1.6.5' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0'
- } else {
- container 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.5--hdfd78af_0' :
+ 'quay.io/biocontainers/plasmidid:1.6.5--hdfd78af_0' }"
input:
tuple val(meta), path(scaffold)
@@ -34,19 +23,20 @@ process PLASMIDID {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
plasmidID \\
-d $fasta \\
-s $prefix \\
-c $scaffold \\
- $options.args \\
+ $args \\
-o .
mv NO_GROUP/$prefix ./$prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(plasmidID --version 2>&1))
+ "${task.process}":
+ plasmidid: \$(echo \$(plasmidID --version 2>&1))
END_VERSIONS
"""
}
diff --git a/modules/plink/extract/functions.nf b/modules/plink/extract/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/plink/extract/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/plink/extract/main.nf b/modules/plink/extract/main.nf
index 2e18500a..34b12fca 100644
--- a/modules/plink/extract/main.nf
+++ b/modules/plink/extract/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PLINK_EXTRACT {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
- } else {
- container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' :
+ 'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }"
input:
tuple val(meta), path(bed), path(bim), path(fam), path(variants)
@@ -28,20 +17,21 @@ process PLINK_EXTRACT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
"""
plink \\
--bfile ${meta.id} \\
- $options.args \\
+ $args \\
--extract $variants \\
--threads $task.cpus \\
--make-bed \\
--out $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
+ "${task.process}":
+ plink: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
END_VERSIONS
"""
}
diff --git a/modules/plink/vcf/functions.nf b/modules/plink/vcf/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/plink/vcf/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/plink/vcf/main.nf b/modules/plink/vcf/main.nf
index a676b723..b6fd03d7 100644
--- a/modules/plink/vcf/main.nf
+++ b/modules/plink/vcf/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PLINK_VCF {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
- } else {
- container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1' :
+ 'quay.io/biocontainers/plink:1.90b6.21--h779adbc_1' }"
input:
tuple val(meta), path(vcf)
@@ -29,18 +18,19 @@ process PLINK_VCF {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
plink \\
--vcf ${vcf} \\
- $options.args \\
+ $args \\
--threads $task.cpus \\
--out ${prefix}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' )
+ "${task.process}":
+ plink: \$(echo \$(plink --version 2>&1) | sed 's/^PLINK v//' | sed 's/..-bit.*//' )
END_VERSIONS
"""
}
diff --git a/modules/plink2/vcf/functions.nf b/modules/plink2/vcf/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/plink2/vcf/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/plink2/vcf/main.nf b/modules/plink2/vcf/main.nf
index 869a5587..8101f7dd 100644
--- a/modules/plink2/vcf/main.nf
+++ b/modules/plink2/vcf/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PLINK2_VCF {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::plink2=2.00a2.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1"
- } else {
- container "quay.io/biocontainers/plink2:2.00a2.3--h712d239_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/plink2:2.00a2.3--h712d239_1' :
+ 'quay.io/biocontainers/plink2:2.00a2.3--h712d239_1' }"
input:
tuple val(meta), path(vcf)
@@ -28,16 +17,17 @@ process PLINK2_VCF {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
plink2 \\
- $options.args \\
+ $args \\
--vcf $vcf \\
--out ${prefix}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
+ "${task.process}":
+ plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
END_VERSIONS
"""
}
diff --git a/modules/pmdtools/filter/functions.nf b/modules/pmdtools/filter/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pmdtools/filter/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pmdtools/filter/main.nf b/modules/pmdtools/filter/main.nf
index 3e363a9c..301f9206 100644
--- a/modules/pmdtools/filter/main.nf
+++ b/modules/pmdtools/filter/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PMDTOOLS_FILTER {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pmdtools=0.60" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5"
- } else {
- container "quay.io/biocontainers/pmdtools:0.60--hdfd78af_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pmdtools:0.60--hdfd78af_5' :
+ 'quay.io/biocontainers/pmdtools:0.60--hdfd78af_5' }"
input:
tuple val(meta), path(bam), path (bai)
@@ -28,8 +17,11 @@ process PMDTOOLS_FILTER {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def args3 = task.ext.args3 ?: ''
def split_cpus = Math.floor(task.cpus/2)
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use the suffix option to disambiguate!"
//threshold and header flags activate filtering function of pmdtools
"""
@@ -37,22 +29,22 @@ process PMDTOOLS_FILTER {
calmd \\
$bam \\
$reference \\
- $options.args \\
+ $args \\
-@ ${split_cpus} \\
| pmdtools \\
--threshold $threshold \\
--header \\
- $options.args2 \\
+ $args2 \\
| samtools \\
view \\
- $options.args3 \\
+ $args3 \\
-Sb \\
- \\
-@ ${split_cpus} \\
-o ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
+ "${task.process}":
pmdtools: \$( pmdtools --version | cut -f2 -d ' ' | sed 's/v//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
diff --git a/modules/porechop/functions.nf b/modules/porechop/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/porechop/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/porechop/main.nf b/modules/porechop/main.nf
index cf564938..2edc5c78 100644
--- a/modules/porechop/main.nf
+++ b/modules/porechop/main.nf
@@ -1,42 +1,32 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PORECHOP {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2"
- } else {
- container "quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
+ 'quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2' }"
input:
tuple val(meta), path(reads)
output:
- tuple val(meta), path("*.fastq.gz") , emit: reads
- path "versions.yml" , emit: versions
+ tuple val(meta), path("*.fastq.gz"), emit: reads
+ path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
porechop \\
- -i ${reads} \\
- -t ${task.cpus} \\
- ${options.args} \\
+ -i $reads \\
+ -t $task.cpus \\
+ $args \\
-o ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( porechop --version )
+ "${task.process}":
+ porechop: \$( porechop --version )
END_VERSIONS
"""
}
diff --git a/modules/preseq/lcextrap/functions.nf b/modules/preseq/lcextrap/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/preseq/lcextrap/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/preseq/lcextrap/main.nf b/modules/preseq/lcextrap/main.nf
index f551a549..43f86cf8 100644
--- a/modules/preseq/lcextrap/main.nf
+++ b/modules/preseq/lcextrap/main.nf
@@ -1,23 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PRESEQ_LCEXTRAP {
tag "$meta.id"
label 'process_medium'
label 'error_ignore'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1"
- } else {
- container "quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1' :
+ 'quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1' }"
input:
tuple val(meta), path(bam)
@@ -28,20 +17,21 @@ process PRESEQ_LCEXTRAP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def paired_end = meta.single_end ? '' : '-pe'
"""
preseq \\
lc_extrap \\
- $options.args \\
+ $args \\
$paired_end \\
-output ${prefix}.ccurve.txt \\
$bam
cp .command.err ${prefix}.command.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
+ "${task.process}":
+ preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/prodigal/functions.nf b/modules/prodigal/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/prodigal/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/prodigal/main.nf b/modules/prodigal/main.nf
index 572ffe92..b09da13c 100644
--- a/modules/prodigal/main.nf
+++ b/modules/prodigal/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PRODIGAL {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2"
- } else {
- container "quay.io/biocontainers/prodigal:2.6.3--h516909a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2' :
+ 'quay.io/biocontainers/prodigal:2.6.3--h516909a_2' }"
input:
tuple val(meta), path(genome)
@@ -30,10 +19,11 @@ process PRODIGAL {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
prodigal -i "${genome}" \\
- $options.args \\
+ $args \\
-f $output_format \\
-d "${prefix}.fna" \\
-o "${prefix}.${output_format}" \\
@@ -41,8 +31,8 @@ process PRODIGAL {
-s "${prefix}_all.txt"
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
+ "${task.process}":
+ prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
END_VERSIONS
"""
}
diff --git a/modules/prokka/functions.nf b/modules/prokka/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/prokka/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/prokka/main.nf b/modules/prokka/main.nf
index fb86078c..8fae6367 100644
--- a/modules/prokka/main.nf
+++ b/modules/prokka/main.nf
@@ -1,21 +1,11 @@
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PROKKA {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl526_0"
- } else {
- container "quay.io/biocontainers/prokka:1.14.6--pl526_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl526_0' :
+ 'quay.io/biocontainers/prokka:1.14.6--pl526_0' }"
input:
tuple val(meta), path(fasta)
@@ -38,12 +28,13 @@ process PROKKA {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
def prodigal_opt = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
"""
prokka \\
- $options.args \\
+ $args \\
--cpus $task.cpus \\
--prefix $prefix \\
$proteins_opt \\
@@ -51,8 +42,8 @@ process PROKKA {
$fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
+ "${task.process}":
+ prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
END_VERSIONS
"""
}
diff --git a/modules/pycoqc/functions.nf b/modules/pycoqc/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pycoqc/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pycoqc/main.nf b/modules/pycoqc/main.nf
index 2c263d61..e966b31c 100644
--- a/modules/pycoqc/main.nf
+++ b/modules/pycoqc/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PYCOQC {
tag "$summary"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::pycoqc=2.5.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0"
- } else {
- container "quay.io/biocontainers/pycoqc:2.5.2--py_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pycoqc:2.5.2--py_0' :
+ 'quay.io/biocontainers/pycoqc:2.5.2--py_0' }"
input:
path summary
@@ -27,16 +16,17 @@ process PYCOQC {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
pycoQC \\
- $options.args \\
+ $args \\
-f $summary \\
-o pycoqc.html \\
-j pycoqc.json
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//')
+ "${task.process}":
+ pycoqc: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/pydamage/analyze/functions.nf b/modules/pydamage/analyze/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pydamage/analyze/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pydamage/analyze/main.nf b/modules/pydamage/analyze/main.nf
index 9cfb8a1a..c55616db 100644
--- a/modules/pydamage/analyze/main.nf
+++ b/modules/pydamage/analyze/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PYDAMAGE_ANALYZE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
+ 'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -26,17 +15,18 @@ process PYDAMAGE_ANALYZE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pydamage \\
analyze \\
- $options.args \\
+ $args \\
-p $task.cpus \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
+ "${task.process}":
+ pydamage: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
END_VERSIONS
"""
}
diff --git a/modules/pydamage/filter/functions.nf b/modules/pydamage/filter/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/pydamage/filter/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/pydamage/filter/main.nf b/modules/pydamage/filter/main.nf
index 6cd7ae7a..2e0afac9 100644
--- a/modules/pydamage/filter/main.nf
+++ b/modules/pydamage/filter/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process PYDAMAGE_FILTER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0"
- } else {
- container "quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
+ 'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
input:
tuple val(meta), path(csv)
@@ -26,17 +15,18 @@ process PYDAMAGE_FILTER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
pydamage \\
filter \\
- $options.args \\
+ $args \\
$csv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
+ "${task.process}":
+ pydamage: \$(echo \$(pydamage --version 2>&1) | sed -e 's/pydamage, version //g')
END_VERSIONS
"""
}
diff --git a/modules/qcat/functions.nf b/modules/qcat/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/qcat/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/qcat/main.nf b/modules/qcat/main.nf
index b650fb8c..9f53f0cb 100644
--- a/modules/qcat/main.nf
+++ b/modules/qcat/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process QCAT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0"
- } else {
- container "quay.io/biocontainers/qcat:1.1.0--py_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' :
+ 'quay.io/biocontainers/qcat:1.1.0--py_0' }"
input:
tuple val(meta), path(reads)
@@ -27,7 +16,8 @@ process QCAT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
## Unzip fastq file
## qcat doesn't support zipped files yet
@@ -47,8 +37,8 @@ process QCAT {
gzip fastq/*
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(qcat --version 2>&1 | sed 's/^.*qcat //; s/ .*\$//')
+ "${task.process}":
+ qcat: \$(qcat --version 2>&1 | sed 's/^.*qcat //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/qualimap/bamqc/functions.nf b/modules/qualimap/bamqc/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/qualimap/bamqc/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf
index d33f1e67..a47fde7e 100644
--- a/modules/qualimap/bamqc/main.nf
+++ b/modules/qualimap/bamqc/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process QUALIMAP_BAMQC {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
- } else {
- container "quay.io/biocontainers/qualimap:2.2.2d--1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' :
+ 'quay.io/biocontainers/qualimap:2.2.2d--1' }"
input:
tuple val(meta), path(bam)
@@ -28,7 +17,8 @@ process QUALIMAP_BAMQC {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
def memory = task.memory.toGiga() + "G"
@@ -47,7 +37,7 @@ process QUALIMAP_BAMQC {
qualimap \\
--java-mem-size=$memory \\
bamqc \\
- $options.args \\
+ $args \\
-bam $bam \\
$regions \\
-p $strandedness \\
@@ -56,8 +46,8 @@ process QUALIMAP_BAMQC {
-nt $task.cpus
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
+ "${task.process}":
+ qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/qualimap/rnaseq/functions.nf b/modules/qualimap/rnaseq/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/qualimap/rnaseq/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf
index 9492cec6..459f3da5 100644
--- a/modules/qualimap/rnaseq/main.nf
+++ b/modules/qualimap/rnaseq/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process QUALIMAP_RNASEQ {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
- } else {
- container "quay.io/biocontainers/qualimap:2.2.2d--1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' :
+ 'quay.io/biocontainers/qualimap:2.2.2d--1' }"
input:
tuple val(meta), path(bam)
@@ -27,7 +16,8 @@ process QUALIMAP_RNASEQ {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def paired_end = meta.single_end ? '' : '-pe'
def memory = task.memory.toGiga() + "G"
@@ -44,7 +34,7 @@ process QUALIMAP_RNASEQ {
qualimap \\
--java-mem-size=$memory \\
rnaseq \\
- $options.args \\
+ $args \\
-bam $bam \\
-gtf $gtf \\
-p $strandedness \\
@@ -52,8 +42,8 @@ process QUALIMAP_RNASEQ {
-outdir $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
+ "${task.process}":
+ qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/quast/functions.nf b/modules/quast/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/quast/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/quast/main.nf b/modules/quast/main.nf
index 072d649d..43caca3d 100644
--- a/modules/quast/main.nf
+++ b/modules/quast/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process QUAST {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::quast=5.0.2' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2'
- } else {
- container 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/quast:5.0.2--py37pl526hb5aa323_2' :
+ 'quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }"
input:
path consensus
@@ -30,7 +19,8 @@ process QUAST {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ?: software
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ?: 'quast'
def features = use_gff ? "--features $gff" : ''
def reference = use_fasta ? "-r $fasta" : ''
"""
@@ -39,12 +29,14 @@ process QUAST {
$reference \\
$features \\
--threads $task.cpus \\
- $options.args \\
+ $args \\
${consensus.join(' ')}
+
ln -s ${prefix}/report.tsv
+
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
+ "${task.process}":
+ quast: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/racon/functions.nf b/modules/racon/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/racon/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/racon/main.nf b/modules/racon/main.nf
index 60a5061e..5936fac0 100644
--- a/modules/racon/main.nf
+++ b/modules/racon/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RACON {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::racon=1.4.20" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1"
- } else {
- container "quay.io/biocontainers/racon:1.4.20--h9a82719_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' :
+ 'quay.io/biocontainers/racon:1.4.20--h9a82719_1' }"
input:
tuple val(meta), path(reads), path(assembly), path(paf)
@@ -26,20 +15,21 @@ process RACON {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- racon -t "${task.cpus}" \\
+ racon -t "$task.cpus" \\
"${reads}" \\
"${paf}" \\
- $options.args \\
+ $args \\
"${assembly}" > \\
${prefix}_assembly_consensus.fasta
gzip -n ${prefix}_assembly_consensus.fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( racon --version 2>&1 | sed 's/^.*v//' )
+ "${task.process}":
+ racon: \$( racon --version 2>&1 | sed 's/^.*v//' )
END_VERSIONS
"""
}
diff --git a/modules/rapidnj/functions.nf b/modules/rapidnj/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rapidnj/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rapidnj/main.nf b/modules/rapidnj/main.nf
index aa23b56e..04a08227 100644
--- a/modules/rapidnj/main.nf
+++ b/modules/rapidnj/main.nf
@@ -1,23 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '2.3.2' // No version information printed
+def VERSION = '2.3.2' // Version information not provided by tool on CLI
process RAPIDNJ {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' :
+ 'quay.io/biocontainers/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' }"
input:
path alignment
@@ -28,20 +17,21 @@ process RAPIDNJ {
path "versions.yml", emit: versions
script:
+ def args = task.ext.args ?: ''
"""
python \\
-c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'
rapidnj \\
alignment.sth \\
- $options.args \\
+ $args \\
-i sth \\
-c $task.cpus \\
-x rapidnj_phylogeny.tre
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ rapidnj: $VERSION
biopython: \$(python -c "import Bio; print(Bio.__version__)")
END_VERSIONS
"""
diff --git a/modules/rasusa/functions.nf b/modules/rasusa/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rasusa/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rasusa/main.nf b/modules/rasusa/main.nf
index b9ba0b13..b43792ee 100644
--- a/modules/rasusa/main.nf
+++ b/modules/rasusa/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RASUSA {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rasusa=0.3.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1"
- } else {
- container "quay.io/biocontainers/rasusa:0.3.0--h779adbc_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1' :
+ 'quay.io/biocontainers/rasusa:0.3.0--h779adbc_1' }"
input:
tuple val(meta), path(reads), val(genome_size)
@@ -27,18 +16,19 @@ process RASUSA {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def output = meta.single_end ? "--output ${prefix}.fastq.gz" : "--output ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz"
"""
rasusa \\
- $options.args \\
+ $args \\
--coverage $depth_cutoff \\
--genome-size $genome_size \\
--input $reads \\
$output
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(rasusa --version 2>&1 | sed -e "s/rasusa //g")
+ "${task.process}":
+ rasusa: \$(rasusa --version 2>&1 | sed -e "s/rasusa //g")
END_VERSIONS
"""
}
diff --git a/modules/raxmlng/functions.nf b/modules/raxmlng/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/raxmlng/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/raxmlng/main.nf b/modules/raxmlng/main.nf
index f607b506..62b6c78a 100644
--- a/modules/raxmlng/main.nf
+++ b/modules/raxmlng/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RAXMLNG {
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::raxml-ng=1.0.3' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0"
- } else {
- container "quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0' :
+ 'quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0' }"
input:
path alignment
@@ -26,16 +15,17 @@ process RAXMLNG {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
raxml-ng \\
- $options.args \\
+ $args \\
--msa $alignment \\
--threads $task.cpus \\
--prefix output
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
+ "${task.process}":
+ raxmlng: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/rmarkdownnotebook/functions.nf b/modules/rmarkdownnotebook/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rmarkdownnotebook/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rmarkdownnotebook/main.nf b/modules/rmarkdownnotebook/main.nf
index 4bded58c..9a7db505 100644
--- a/modules/rmarkdownnotebook/main.nf
+++ b/modules/rmarkdownnotebook/main.nf
@@ -1,29 +1,16 @@
-// Import generic module functions
-include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
-include { dump_params_yml; indent_code_block } from "./parametrize"
-
-params.options = [:]
-options = initOptions(params.options)
-params.parametrize = true
-params.implicit_params = true
-params.meta_params = true
+include { dump_params_yml; indent_code_block } from "./parametrize"
process RMARKDOWNNOTEBOOK {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
//NB: You likely want to override this with a container containing all required
//dependencies for your analysis. The container at least needs to contain the
//yaml and rmarkdown R packages.
conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
+ 'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }"
input:
tuple val(meta), path(notebook)
@@ -37,7 +24,11 @@ process RMARKDOWNNOTEBOOK {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def parametrize = (task.ext.parametrize == null) ? true : task.ext.parametrize
+ def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
+ def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
// Dump parameters to yaml file.
// Using a yaml file over using the CLI params because
@@ -45,14 +36,14 @@ process RMARKDOWNNOTEBOOK {
// * allows to pass nested maps instead of just single values
def params_cmd = ""
def render_cmd = ""
- if (params.parametrize) {
+ if (parametrize) {
nb_params = [:]
- if (params.implicit_params) {
+ if (implicit_params) {
nb_params["cpus"] = task.cpus
nb_params["artifact_dir"] = "artifacts"
nb_params["input_dir"] = "./"
}
- if (params.meta_params) {
+ if (meta_params) {
nb_params["meta"] = meta
}
nb_params += parameters
@@ -73,9 +64,9 @@ process RMARKDOWNNOTEBOOK {
mkdir artifacts
# Set parallelism for BLAS/MKL etc. to avoid over-booking of resources
- export MKL_NUM_THREADS="${task.cpus}"
- export OPENBLAS_NUM_THREADS="${task.cpus}"
- export OMP_NUM_THREADS="${task.cpus}"
+ export MKL_NUM_THREADS="$task.cpus"
+ export OPENBLAS_NUM_THREADS="$task.cpus"
+ export OMP_NUM_THREADS="$task.cpus"
# Work around https://github.com/rstudio/rmarkdown/issues/1508
# If the symbolic link is not replaced by a physical file
@@ -90,7 +81,7 @@ process RMARKDOWNNOTEBOOK {
EOF
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
+ "${task.process}":
rmarkdown: \$(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))")
END_VERSIONS
"""
diff --git a/modules/roary/functions.nf b/modules/roary/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/roary/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/roary/main.nf b/modules/roary/main.nf
index 9dc948fb..a05973eb 100644
--- a/modules/roary/main.nf
+++ b/modules/roary/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process ROARY {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::roary=3.13.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0"
- } else {
- container "quay.io/biocontainers/roary:3.13.0--pl526h516909a_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' :
+ 'quay.io/biocontainers/roary:3.13.0--pl526h516909a_0' }"
input:
tuple val(meta), path(gff)
@@ -27,17 +16,18 @@ process ROARY {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
roary \\
- $options.args \\
+ $args \\
-p $task.cpus \\
-f results/ \\
$gff
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( roary --version )
+ "${task.process}":
+ roary: \$( roary --version )
END_VERSIONS
"""
}
diff --git a/modules/rsem/calculateexpression/functions.nf b/modules/rsem/calculateexpression/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rsem/calculateexpression/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf
index f19392f7..659082fa 100644
--- a/modules/rsem/calculateexpression/main.nf
+++ b/modules/rsem/calculateexpression/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEM_CALCULATEEXPRESSION {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
+ 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
input:
tuple val(meta), path(reads)
@@ -34,7 +23,8 @@ process RSEM_CALCULATEEXPRESSION {
tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {
@@ -50,14 +40,14 @@ process RSEM_CALCULATEEXPRESSION {
--temporary-folder ./tmp/ \\
$strandedness \\
$paired_end \\
- $options.args \\
+ $args \\
$reads \\
\$INDEX \\
$prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+ "${task.process}":
+ rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
diff --git a/modules/rsem/preparereference/functions.nf b/modules/rsem/preparereference/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rsem/preparereference/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf
index 7e671207..95597b74 100644
--- a/modules/rsem/preparereference/main.nf
+++ b/modules/rsem/preparereference/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEM_PREPAREREFERENCE {
tag "$fasta"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
+ 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
input:
path fasta, stageAs: "rsem/*"
@@ -28,9 +17,11 @@ process RSEM_PREPAREREFERENCE {
path "versions.yml" , emit: versions
script:
- def args = options.args.tokenize()
- if (args.contains('--star')) {
- args.removeIf { it.contains('--star') }
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def args_list = args.tokenize()
+ if (args_list.contains('--star')) {
+ args_list.removeIf { it.contains('--star') }
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
"""
STAR \\
@@ -40,18 +31,18 @@ process RSEM_PREPAREREFERENCE {
--sjdbGTFfile $gtf \\
--runThreadN $task.cpus \\
$memory \\
- $options.args2
+ $args2
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\
- ${args.join(' ')} \\
+ ${args_list.join(' ')} \\
$fasta \\
rsem/genome
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+ "${task.process}":
+ rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
@@ -60,13 +51,13 @@ process RSEM_PREPAREREFERENCE {
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\
- $options.args \\
+ $args \\
$fasta \\
rsem/genome
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
+ "${task.process}":
+ rsem: \$(rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g")
star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
diff --git a/modules/rseqc/bamstat/functions.nf b/modules/rseqc/bamstat/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/bamstat/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/bamstat/main.nf b/modules/rseqc/bamstat/main.nf
index 64939add..d9d3fa36 100644
--- a/modules/rseqc/bamstat/main.nf
+++ b/modules/rseqc/bamstat/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_BAMSTAT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -26,16 +15,17 @@ process RSEQC_BAMSTAT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
bam_stat.py \\
-i $bam \\
- $options.args \\
+ $args \\
> ${prefix}.bam_stat.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
+ "${task.process}":
+ rseqc: \$(bam_stat.py --version | sed -e "s/bam_stat.py //g")
END_VERSIONS
"""
}
diff --git a/modules/rseqc/inferexperiment/functions.nf b/modules/rseqc/inferexperiment/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/inferexperiment/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/inferexperiment/main.nf b/modules/rseqc/inferexperiment/main.nf
index c5e94943..3b879cfb 100644
--- a/modules/rseqc/inferexperiment/main.nf
+++ b/modules/rseqc/inferexperiment/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_INFEREXPERIMENT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -27,17 +16,18 @@ process RSEQC_INFEREXPERIMENT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
infer_experiment.py \\
-i $bam \\
-r $bed \\
- $options.args \\
+ $args \\
> ${prefix}.infer_experiment.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
+ "${task.process}":
+ rseqc: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
END_VERSIONS
"""
}
diff --git a/modules/rseqc/innerdistance/functions.nf b/modules/rseqc/innerdistance/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/innerdistance/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/innerdistance/main.nf b/modules/rseqc/innerdistance/main.nf
index 622cd5cd..88bec499 100644
--- a/modules/rseqc/innerdistance/main.nf
+++ b/modules/rseqc/innerdistance/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_INNERDISTANCE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -31,27 +20,28 @@ process RSEQC_INNERDISTANCE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (!meta.single_end) {
"""
inner_distance.py \\
-i $bam \\
-r $bed \\
-o $prefix \\
- $options.args \\
+ $args \\
> stdout.txt
head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
+ "${task.process}":
+ rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
END_VERSIONS
"""
} else {
"""
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
+ "${task.process}":
+ rseqc: \$(inner_distance.py --version | sed -e "s/inner_distance.py //g")
END_VERSIONS
"""
}
diff --git a/modules/rseqc/junctionannotation/functions.nf b/modules/rseqc/junctionannotation/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/junctionannotation/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/junctionannotation/main.nf b/modules/rseqc/junctionannotation/main.nf
index 1b75d915..b6949641 100644
--- a/modules/rseqc/junctionannotation/main.nf
+++ b/modules/rseqc/junctionannotation/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_JUNCTIONANNOTATION {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -33,18 +22,19 @@ process RSEQC_JUNCTIONANNOTATION {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
junction_annotation.py \\
-i $bam \\
-r $bed \\
-o $prefix \\
- $options.args \\
+ $args \\
2> ${prefix}.junction_annotation.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
+ "${task.process}":
+ rseqc: \$(junction_annotation.py --version | sed -e "s/junction_annotation.py //g")
END_VERSIONS
"""
}
diff --git a/modules/rseqc/junctionsaturation/functions.nf b/modules/rseqc/junctionsaturation/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/junctionsaturation/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/junctionsaturation/main.nf b/modules/rseqc/junctionsaturation/main.nf
index fa435aea..58451d2e 100644
--- a/modules/rseqc/junctionsaturation/main.nf
+++ b/modules/rseqc/junctionsaturation/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_JUNCTIONSATURATION {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -28,17 +17,18 @@ process RSEQC_JUNCTIONSATURATION {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
junction_saturation.py \\
-i $bam \\
-r $bed \\
-o $prefix \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
+ "${task.process}":
+ rseqc: \$(junction_saturation.py --version | sed -e "s/junction_saturation.py //g")
END_VERSIONS
"""
}
diff --git a/modules/rseqc/readdistribution/functions.nf b/modules/rseqc/readdistribution/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/readdistribution/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/readdistribution/main.nf b/modules/rseqc/readdistribution/main.nf
index 0c83fdf0..74af618d 100644
--- a/modules/rseqc/readdistribution/main.nf
+++ b/modules/rseqc/readdistribution/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_READDISTRIBUTION {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -27,7 +16,8 @@ process RSEQC_READDISTRIBUTION {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
read_distribution.py \\
-i $bam \\
@@ -35,8 +25,8 @@ process RSEQC_READDISTRIBUTION {
> ${prefix}.read_distribution.txt
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g")
+ "${task.process}":
+ rseqc: \$(read_distribution.py --version | sed -e "s/read_distribution.py //g")
END_VERSIONS
"""
}
diff --git a/modules/rseqc/readduplication/functions.nf b/modules/rseqc/readduplication/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/rseqc/readduplication/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/rseqc/readduplication/main.nf b/modules/rseqc/readduplication/main.nf
index bee82682..80fcb150 100644
--- a/modules/rseqc/readduplication/main.nf
+++ b/modules/rseqc/readduplication/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process RSEQC_READDUPLICATION {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
- } else {
- container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1' :
+ 'quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1' }"
input:
tuple val(meta), path(bam)
@@ -29,16 +18,17 @@ process RSEQC_READDUPLICATION {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
read_duplication.py \\
-i $bam \\
-o $prefix \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
+ "${task.process}":
+ rseqc: \$(read_duplication.py --version | sed -e "s/read_duplication.py //g")
END_VERSIONS
"""
}
diff --git a/modules/salmon/index/functions.nf b/modules/salmon/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/salmon/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/salmon/index/main.nf b/modules/salmon/index/main.nf
index c3fcef01..b0a2f973 100644
--- a/modules/salmon/index/main.nf
+++ b/modules/salmon/index/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SALMON_INDEX {
tag "$transcript_fasta"
label "process_medium"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
- } else {
- container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' :
+ 'quay.io/biocontainers/salmon:1.5.2--h84f40af_0' }"
input:
path genome_fasta
@@ -27,6 +16,7 @@ process SALMON_INDEX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
def gentrome = "gentrome.fa"
if (genome_fasta.endsWith('.gz')) {
@@ -43,11 +33,11 @@ process SALMON_INDEX {
--threads $task.cpus \\
-t $gentrome \\
-d decoys.txt \\
- $options.args \\
+ $args \\
-i salmon
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
+ "${task.process}":
+ salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
"""
}
diff --git a/modules/salmon/quant/functions.nf b/modules/salmon/quant/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/salmon/quant/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/salmon/quant/main.nf b/modules/salmon/quant/main.nf
index 7c2e0e17..9557fd24 100644
--- a/modules/salmon/quant/main.nf
+++ b/modules/salmon/quant/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SALMON_QUANT {
tag "$meta.id"
label "process_medium"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
- } else {
- container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' :
+ 'quay.io/biocontainers/salmon:1.5.2--h84f40af_0' }"
input:
tuple val(meta), path(reads)
@@ -31,7 +20,8 @@ process SALMON_QUANT {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def reference = "--index $index"
def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
@@ -68,12 +58,12 @@ process SALMON_QUANT {
--libType=$strandedness \\
$reference \\
$input_reads \\
- $options.args \\
+ $args \\
-o $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
+ "${task.process}":
+ salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
"""
}
diff --git a/modules/samblaster/functions.nf b/modules/samblaster/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samblaster/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samblaster/main.nf b/modules/samblaster/main.nf
index 4481d8cd..8445b0d0 100644
--- a/modules/samblaster/main.nf
+++ b/modules/samblaster/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMBLASTER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samblaster=0.1.26 bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' :
+ 'quay.io/biocontainers/mulled-v2-19fa9f1a5c3966b63a24166365e81da35738c5ab:ba4a02b56f3e524a6e006bcd99fe8cc1d7fe09eb-0' }"
input:
tuple val(meta), path(bam)
@@ -26,16 +15,19 @@ process SAMBLASTER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def args3 = task.ext.args3 ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate"
"""
- samtools view -h $options.args2 $bam | \\
- samblaster $options.args | \\
- samtools view $options.args3 -Sb - >${prefix}.bam
+ samtools view -h $args2 $bam | \\
+ samblaster $args | \\
+ samtools view $args3 -Sb - >${prefix}.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( samblaster -h 2>&1 | head -n 1 | sed 's/^samblaster: Version //' )
+ "${task.process}":
+ samblaster: \$( samblaster -h 2>&1 | head -n 1 | sed 's/^samblaster: Version //' )
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
diff --git a/modules/samtools/ampliconclip/functions.nf b/modules/samtools/ampliconclip/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/ampliconclip/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf
index 4cf98d3f..87d6ff8b 100644
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_AMPLICONCLIP {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
@@ -31,13 +20,14 @@ process SAMTOOLS_AMPLICONCLIP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
"""
samtools \\
ampliconclip \\
- $options.args \\
+ $args \\
$rejects \\
$stats \\
-b $bed \\
@@ -45,8 +35,8 @@ process SAMTOOLS_AMPLICONCLIP {
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/bam2fq/functions.nf b/modules/samtools/bam2fq/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/bam2fq/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf
index 48e3249c..20e83a14 100644
--- a/modules/samtools/bam2fq/main.nf
+++ b/modules/samtools/bam2fq/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_BAM2FQ {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(inputbam)
@@ -27,13 +16,14 @@ process SAMTOOLS_BAM2FQ {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (split){
"""
samtools \\
bam2fq \\
- $options.args \\
+ $args \\
-@ $task.cpus \\
-1 ${prefix}_1.fq.gz \\
-2 ${prefix}_2.fq.gz \\
@@ -42,21 +32,21 @@ process SAMTOOLS_BAM2FQ {
$inputbam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} else {
"""
samtools \\
bam2fq \\
- $options.args \\
+ $args \\
-@ $task.cpus \\
$inputbam >${prefix}_interleaved.fq.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/depth/functions.nf b/modules/samtools/depth/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/depth/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/depth/main.nf b/modules/samtools/depth/main.nf
index 9c46b011..f336547f 100644
--- a/modules/samtools/depth/main.nf
+++ b/modules/samtools/depth/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_DEPTH {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
@@ -26,18 +15,19 @@ process SAMTOOLS_DEPTH {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
samtools \\
depth \\
- $options.args \\
+ $args \\
-o ${prefix}.tsv \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/faidx/functions.nf b/modules/samtools/faidx/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/faidx/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf
index 80708084..c53373a9 100644
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_FAIDX {
tag "$fasta"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
path fasta
@@ -26,11 +15,12 @@ process SAMTOOLS_FAIDX {
path "versions.yml", emit: versions
script:
+ def args = task.ext.args ?: ''
"""
samtools faidx $fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/fastq/functions.nf b/modules/samtools/fastq/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/fastq/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf
index fb7e3904..bdbf53e4 100644
--- a/modules/samtools/fastq/main.nf
+++ b/modules/samtools/fastq/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_FASTQ {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
@@ -26,18 +15,19 @@ process SAMTOOLS_FASTQ {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
"""
samtools fastq \\
- $options.args \\
+ $args \\
--threads ${task.cpus-1} \\
$endedness \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/fixmate/functions.nf b/modules/samtools/fixmate/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/fixmate/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf
index af1cf829..180833f4 100644
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_FIXMATE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
@@ -26,20 +15,21 @@ process SAMTOOLS_FIXMATE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use the suffix option to disambiguate!"
"""
samtools \\
fixmate \\
- $options.args \\
+ $args \\
--threads ${task.cpus-1} \\
$bam \\
${prefix}.bam \\
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/flagstat/functions.nf b/modules/samtools/flagstat/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/flagstat/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf
index 072a135f..03721d0b 100644
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -26,11 +15,12 @@ process SAMTOOLS_FLAGSTAT {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/idxstats/functions.nf b/modules/samtools/idxstats/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/idxstats/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf
index fa0e7dc3..cd068679 100644
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_IDXSTATS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -26,11 +15,12 @@ process SAMTOOLS_IDXSTATS {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
samtools idxstats $bam > ${bam}.idxstats
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/index/functions.nf b/modules/samtools/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf
index d66e4513..b033e225 100644
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_INDEX {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(input)
@@ -28,12 +17,13 @@ process SAMTOOLS_INDEX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
- samtools index -@ ${task.cpus-1} $options.args $input
+ samtools index -@ ${task.cpus-1} $args $input
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/merge/functions.nf b/modules/samtools/merge/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/merge/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf
index ab641bb9..8eeb64a2 100644
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_MERGE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(input_files)
@@ -28,15 +17,16 @@ process SAMTOOLS_MERGE {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def file_type = input_files[0].getExtension()
def reference = fasta ? "--reference ${fasta}" : ""
"""
- samtools merge --threads ${task.cpus-1} $options.args ${reference} ${prefix}.${file_type} $input_files
+ samtools merge --threads ${task.cpus-1} $args ${reference} ${prefix}.${file_type} $input_files
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/mpileup/functions.nf b/modules/samtools/mpileup/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/mpileup/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf
index 081682ed..5f6e2d49 100644
--- a/modules/samtools/mpileup/main.nf
+++ b/modules/samtools/mpileup/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_MPILEUP {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
@@ -27,16 +16,17 @@ process SAMTOOLS_MPILEUP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
samtools mpileup \\
--fasta-ref $fasta \\
--output ${prefix}.mpileup \\
- $options.args \\
+ $args \\
$bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/sort/functions.nf b/modules/samtools/sort/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/sort/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf
index f980b472..623f10b6 100644
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_SORT {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam)
@@ -26,12 +15,13 @@ process SAMTOOLS_SORT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+ samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/stats/functions.nf b/modules/samtools/stats/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/stats/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf
index e0a2b50d..83c87002 100644
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_STATS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(input), path(input_index)
@@ -27,13 +16,14 @@ process SAMTOOLS_STATS {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def reference = fasta ? "--reference ${fasta}" : ""
"""
samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/samtools/view/functions.nf b/modules/samtools/view/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/samtools/view/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index e5ff5546..464edd09 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SAMTOOLS_VIEW {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
- } else {
- container "quay.io/biocontainers/samtools:1.14--hb421002_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
+ 'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(input)
@@ -28,15 +17,16 @@ process SAMTOOLS_VIEW {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def reference = fasta ? "--reference ${fasta} -C" : ""
def file_type = input.getExtension()
"""
- samtools view --threads ${task.cpus-1} ${reference} $options.args $input > ${prefix}.${file_type}
+ samtools view --threads ${task.cpus-1} ${reference} $args $input > ${prefix}.${file_type}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+ "${task.process}":
+ samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/scoary/functions.nf b/modules/scoary/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/scoary/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/scoary/main.nf b/modules/scoary/main.nf
index 5720b4e5..8fed0119 100644
--- a/modules/scoary/main.nf
+++ b/modules/scoary/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SCOARY {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2"
- } else {
- container "quay.io/biocontainers/scoary:1.6.16--py_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' :
+ 'quay.io/biocontainers/scoary:1.6.16--py_2' }"
input:
tuple val(meta), path(genes), path(traits)
@@ -27,19 +16,20 @@ process SCOARY {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def newick_tree = tree ? "-n ${tree}" : ""
"""
scoary \\
- $options.args \\
+ $args \\
--no-time \\
--threads $task.cpus \\
--traits $traits \\
--genes $genes
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( scoary --version 2>&1 )
+ "${task.process}":
+ scoary: \$( scoary --version 2>&1 )
END_VERSIONS
"""
}
diff --git a/modules/seacr/callpeak/functions.nf b/modules/seacr/callpeak/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seacr/callpeak/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seacr/callpeak/main.nf b/modules/seacr/callpeak/main.nf
index 97bf1c0b..328e4e6c 100644
--- a/modules/seacr/callpeak/main.nf
+++ b/modules/seacr/callpeak/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '1.3'
+def VERSION = '1.3' // Version information not provided by tool on CLI
process SEACR_CALLPEAK {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0"
- } else {
- container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' :
+ 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' }"
input:
tuple val(meta), path(bedgraph), path(ctrlbedgraph)
@@ -29,17 +18,19 @@ process SEACR_CALLPEAK {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
"""
SEACR_1.3.sh \\
$bedgraph \\
$function_switch \\
- $options.args \\
+ $args \\
$prefix
+
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ seacr: $VERSION
bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
END_VERSIONS
diff --git a/modules/seqkit/split2/functions.nf b/modules/seqkit/split2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seqkit/split2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seqkit/split2/main.nf b/modules/seqkit/split2/main.nf
index 80f55bb6..fc027793 100644
--- a/modules/seqkit/split2/main.nf
+++ b/modules/seqkit/split2/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQKIT_SPLIT2 {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::seqkit=0.16.1' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
- } else {
- container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0' :
+ 'quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0' }"
input:
tuple val(meta), path(reads)
@@ -26,34 +15,35 @@ process SEQKIT_SPLIT2 {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if(meta.single_end){
"""
seqkit \\
split2 \\
- $options.args \\
+ $args \\
--threads $task.cpus \\
-1 $reads \\
--out-dir $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
} else {
"""
seqkit \\
split2 \\
- $options.args \\
+ $args \\
--threads $task.cpus \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
--out-dir $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/seqsero2/functions.nf b/modules/seqsero2/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seqsero2/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seqsero2/main.nf b/modules/seqsero2/main.nf
index 3748a6e4..a8dd731e 100644
--- a/modules/seqsero2/main.nf
+++ b/modules/seqsero2/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQSERO2 {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0"
- } else {
- container "quay.io/biocontainers/seqsero2:1.2.1--py_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' :
+ 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }"
input:
tuple val(meta), path(seqs)
@@ -28,18 +17,19 @@ process SEQSERO2 {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
SeqSero2_package.py \\
- $options.args \\
+ $args \\
-d results/ \\
-n $prefix \\
-p $task.cpus \\
-i $seqs
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
+ "${task.process}":
+ seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
END_VERSIONS
"""
}
diff --git a/modules/seqtk/mergepe/functions.nf b/modules/seqtk/mergepe/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seqtk/mergepe/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seqtk/mergepe/main.nf b/modules/seqtk/mergepe/main.nf
index fb8eb382..954bed5c 100644
--- a/modules/seqtk/mergepe/main.nf
+++ b/modules/seqtk/mergepe/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQTK_MERGEPE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
- } else {
- container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
+ 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
input:
tuple val(meta), path(reads)
@@ -26,27 +15,28 @@ process SEQTK_MERGEPE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
ln -s ${reads} ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
} else {
"""
seqtk \\
mergepe \\
- $options.args \\
+ $args \\
${reads} \\
| gzip -n >> ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/seqtk/sample/functions.nf b/modules/seqtk/sample/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seqtk/sample/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seqtk/sample/main.nf b/modules/seqtk/sample/main.nf
index 3b039fb9..83a107d0 100644
--- a/modules/seqtk/sample/main.nf
+++ b/modules/seqtk/sample/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQTK_SAMPLE {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
- } else {
- container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
+ 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
input:
tuple val(meta), path(reads)
@@ -27,43 +16,44 @@ process SEQTK_SAMPLE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
seqtk \\
sample \\
- $options.args \\
+ $args \\
$reads \\
$sample_size \\
| gzip --no-name > ${prefix}.fastq.gz \\
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
} else {
- if (!(options.args ==~ /.*-s[0-9]+.*/)) {
- options.args = options.args + " -s100"
+ if (!(args ==~ /.*-s[0-9]+.*/)) {
+ args += " -s100"
}
"""
seqtk \\
sample \\
- $options.args \\
+ $args \\
${reads[0]} \\
$sample_size \\
| gzip --no-name > ${prefix}_1.fastq.gz \\
seqtk \\
sample \\
- $options.args \\
+ $args \\
${reads[1]} \\
$sample_size \\
| gzip --no-name > ${prefix}_2.fastq.gz \\
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/seqtk/subseq/functions.nf b/modules/seqtk/subseq/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seqtk/subseq/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seqtk/subseq/main.nf b/modules/seqtk/subseq/main.nf
index df8783de..1d93b061 100644
--- a/modules/seqtk/subseq/main.nf
+++ b/modules/seqtk/subseq/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQTK_SUBSEQ {
tag '$sequences'
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
- } else {
- container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
+ 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
input:
path sequences
@@ -27,7 +16,8 @@ process SEQTK_SUBSEQ {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ?: ''
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ?: ''
def ext = "fa"
if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
ext = "fq"
@@ -35,14 +25,14 @@ process SEQTK_SUBSEQ {
"""
seqtk \\
subseq \\
- $options.args \\
+ $args \\
$sequences \\
$filter_list | \\
gzip --no-name > ${sequences}${prefix}.${ext}.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/sequenzautils/bam2seqz/functions.nf b/modules/sequenzautils/bam2seqz/functions.nf
deleted file mode 100755
index 85628ee0..00000000
--- a/modules/sequenzautils/bam2seqz/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/sequenzautils/bam2seqz/main.nf b/modules/sequenzautils/bam2seqz/main.nf
index 61ca70c6..9082d426 100644
--- a/modules/sequenzautils/bam2seqz/main.nf
+++ b/modules/sequenzautils/bam2seqz/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQUENZAUTILS_BAM2SEQZ {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2"
- } else {
- container "quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' :
+ 'quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }"
input:
tuple val(meta), path(normalbam), path(tumourbam)
@@ -28,11 +17,12 @@ process SEQUENZAUTILS_BAM2SEQZ {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
sequenza-utils \\
bam2seqz \\
- $options.args \\
+ $args \\
-n $normalbam \\
-t $tumourbam \\
--fasta $fasta \\
@@ -40,8 +30,8 @@ process SEQUENZAUTILS_BAM2SEQZ {
-o ${prefix}.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
+ "${task.process}":
+ sequenzautils: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/sequenzautils/gcwiggle/functions.nf b/modules/sequenzautils/gcwiggle/functions.nf
deleted file mode 100755
index 85628ee0..00000000
--- a/modules/sequenzautils/gcwiggle/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/sequenzautils/gcwiggle/main.nf b/modules/sequenzautils/gcwiggle/main.nf
index c952bb70..43358c43 100644
--- a/modules/sequenzautils/gcwiggle/main.nf
+++ b/modules/sequenzautils/gcwiggle/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SEQUENZAUTILS_GCWIGGLE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::sequenza-utils=3.0.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2"
- } else {
- container "quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/sequenza-utils:3.0.0--py38h6ed170a_2' :
+ 'quay.io/biocontainers/sequenza-utils:3.0.0--py38h6ed170a_2' }"
input:
tuple val(meta), path(fasta)
@@ -26,17 +15,18 @@ process SEQUENZAUTILS_GCWIGGLE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
sequenza-utils \\
gc_wiggle \\
- $options.args \\
+ $args \\
--fasta $fasta \\
-o ${prefix}.wig.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
+ "${task.process}":
+ sequenzautils: \$(echo \$(sequenza-utils 2>&1) | sed 's/^.*is version //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/seqwish/induce/functions.nf b/modules/seqwish/induce/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/seqwish/induce/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/seqwish/induce/main.nf b/modules/seqwish/induce/main.nf
index aaabce51..fb25a96e 100644
--- a/modules/seqwish/induce/main.nf
+++ b/modules/seqwish/induce/main.nf
@@ -1,24 +1,14 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '0.7.1'
+def VERSION = '0.7.1' // Version information not provided by tool on CLI
process SEQWISH_INDUCE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::seqwish=0.7.1' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/seqwish:0.7.1--h2e03b76_0"
- } else {
- container "quay.io/biocontainers/seqwish:0.7.1--h2e03b76_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/seqwish:0.7.1--h2e03b76_0' :
+ 'quay.io/biocontainers/seqwish:0.7.1--h2e03b76_0' }"
input:
tuple val(meta), path(paf), path(fasta)
@@ -27,20 +17,20 @@ process SEQWISH_INDUCE {
tuple val(meta), path("*.gfa"), emit: gfa
path "versions.yml" , emit: versions
-
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
seqwish \\
--threads $task.cpus \\
--paf-alns=$paf \\
--seqs=$fasta \\
--gfa=${prefix}.gfa \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ seqwish: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/shovill/functions.nf b/modules/shovill/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/shovill/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/shovill/main.nf b/modules/shovill/main.nf
index 48425f9f..1a56df27 100644
--- a/modules/shovill/main.nf
+++ b/modules/shovill/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SHOVILL {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/shovill:1.1.0--0"
- } else {
- container "quay.io/biocontainers/shovill:1.1.0--0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' :
+ 'quay.io/biocontainers/shovill:1.1.0--0' }"
input:
tuple val(meta), path(reads)
@@ -30,20 +19,21 @@ process SHOVILL {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def memory = task.memory.toGiga()
"""
shovill \\
--R1 ${reads[0]} \\
--R2 ${reads[1]} \\
- $options.args \\
+ $args \\
--cpus $task.cpus \\
--ram $memory \\
--outdir ./ \\
--force
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
+ "${task.process}":
+ shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
END_VERSIONS
"""
}
diff --git a/modules/snpdists/functions.nf b/modules/snpdists/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/snpdists/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/snpdists/main.nf b/modules/snpdists/main.nf
index 506a922a..de79e89b 100644
--- a/modules/snpdists/main.nf
+++ b/modules/snpdists/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SNPDISTS {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::snp-dists=0.8.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0"
- } else {
- container "quay.io/biocontainers/snp-dists:0.8.2--h5bf99c6_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/snp-dists:0.8.2--h5bf99c6_0' :
+ 'quay.io/biocontainers/snp-dists:0.8.2--h5bf99c6_0' }"
input:
tuple val(meta), path(alignment)
@@ -26,15 +15,16 @@ process SNPDISTS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
snp-dists \\
- $options.args \\
+ $args \\
$alignment > ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(snp-dists -v 2>&1 | sed 's/snp-dists //;')
+ "${task.process}":
+ snpdists: \$(snp-dists -v 2>&1 | sed 's/snp-dists //;')
END_VERSIONS
"""
}
diff --git a/modules/snpeff/functions.nf b/modules/snpeff/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/snpeff/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf
index 3a1f6a52..2cd023f6 100644
--- a/modules/snpeff/main.nf
+++ b/modules/snpeff/main.nf
@@ -1,26 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-params.use_cache = false
-params.snpeff_tag = ""
-
process SNPEFF {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::snpeff=5.0" : null)
- if (params.use_cache) {
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1"
- } else {
- container "quay.io/biocontainers/snpeff:5.0--hdfd78af_1"
- }
+ if (task.ext.use_cache) {
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/snpeff:5.0--hdfd78af_1' :
+ 'quay.io/biocontainers/snpeff:5.0--hdfd78af_1' }"
} else {
- container "nfcore/snpeff:${params.snpeff_tag}"
+ container "nfcore/snpeff:${task.ext.snpeff_tag}"
}
input:
@@ -34,26 +21,28 @@ process SNPEFF {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def avail_mem = 6
if (!task.memory) {
log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
- cache = params.use_cache ? "-dataDir \${PWD}/${snpeff_cache}" : ""
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def dir_cache = task.ext.use_cache ? "-dataDir \${PWD}/${cache}" : ""
"""
- snpEff -Xmx${avail_mem}g \\
+ snpEff \\
+ -Xmx${avail_mem}g \\
$db \\
- $options.args \\
+ $args \\
-csvStats ${prefix}.csv \\
- $cache \\
+ $dir_cache \\
$vcf \\
> ${prefix}.ann.vcf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
+ "${task.process}":
+ snpeff: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
END_VERSIONS
"""
}
diff --git a/modules/snpsites/functions.nf b/modules/snpsites/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/snpsites/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/snpsites/main.nf b/modules/snpsites/main.nf
index 543ee01c..60e694ac 100644
--- a/modules/snpsites/main.nf
+++ b/modules/snpsites/main.nf
@@ -1,21 +1,10 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SNPSITES {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::snp-sites=2.5.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0"
- } else {
- container "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0' :
+ 'quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0' }"
input:
path alignment
@@ -27,10 +16,11 @@ process SNPSITES {
env CONSTANT_SITES, emit: constant_sites_string
script:
+ def args = task.ext.args ?: ''
"""
snp-sites \\
$alignment \\
- $options.args \\
+ $args \\
> filtered_alignment.fas
echo \$(snp-sites -C $alignment) > constant.sites.txt
@@ -38,8 +28,8 @@ process SNPSITES {
CONSTANT_SITES=\$(cat constant.sites.txt)
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
+ "${task.process}":
+ snpsites: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
END_VERSIONS
"""
}
diff --git a/modules/sortmerna/functions.nf b/modules/sortmerna/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/sortmerna/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/sortmerna/main.nf b/modules/sortmerna/main.nf
index 9602bb53..83cd8092 100644
--- a/modules/sortmerna/main.nf
+++ b/modules/sortmerna/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SORTMERNA {
tag "$meta.id"
label "process_high"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::sortmerna=4.3.4" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0"
- } else {
- container "quay.io/biocontainers/sortmerna:4.3.4--h9ee0642_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/sortmerna:4.3.4--h9ee0642_0' :
+ 'quay.io/biocontainers/sortmerna:4.3.4--h9ee0642_0' }"
input:
tuple val(meta), path(reads)
@@ -28,7 +17,8 @@ process SORTMERNA {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
sortmerna \\
@@ -38,14 +28,14 @@ process SORTMERNA {
--workdir . \\
--aligned rRNA_reads \\
--other non_rRNA_reads \\
- $options.args
+ $args
mv non_rRNA_reads.fq.gz ${prefix}.fastq.gz
mv rRNA_reads.log ${prefix}.sortmerna.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
+ "${task.process}":
+ sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
END_VERSIONS
"""
} else {
@@ -60,15 +50,15 @@ process SORTMERNA {
--other non_rRNA_reads \\
--paired_in \\
--out2 \\
- $options.args
+ $args
mv non_rRNA_reads_fwd.fq.gz ${prefix}_1.fastq.gz
mv non_rRNA_reads_rev.fq.gz ${prefix}_2.fastq.gz
mv rRNA_reads.log ${prefix}.sortmerna.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
+ "${task.process}":
+ sortmerna: \$(echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/spades/functions.nf b/modules/spades/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/spades/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/spades/main.nf b/modules/spades/main.nf
index 836efbda..4663ec55 100644
--- a/modules/spades/main.nf
+++ b/modules/spades/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SPADES {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0"
- } else {
- container "quay.io/biocontainers/spades:3.15.3--h95f258a_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
+ 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
input:
tuple val(meta), path(illumina), path(pacbio), path(nanopore)
@@ -32,7 +21,8 @@ process SPADES {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def maxmem = task.memory.toGiga()
def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
def pacbio_reads = pacbio ? "--pacbio $pacbio" : ""
@@ -40,7 +30,7 @@ process SPADES {
def custom_hmms = hmm ? "--custom-hmms $hmm" : ""
"""
spades.py \\
- $options.args \\
+ $args \\
--threads $task.cpus \\
--memory $maxmem \\
$custom_hmms \\
@@ -73,8 +63,8 @@ process SPADES {
fi
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
+ "${task.process}":
+ spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/spatyper/functions.nf b/modules/spatyper/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/spatyper/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/spatyper/main.nf b/modules/spatyper/main.nf
index 34207dbf..d7c75ba6 100644
--- a/modules/spatyper/main.nf
+++ b/modules/spatyper/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SPATYPER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/spatyper%3A0.3.3--pyhdfd78af_3"
- } else {
- container "quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/spatyper%3A0.3.3--pyhdfd78af_3' :
+ 'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3' }"
input:
tuple val(meta), path(fasta)
@@ -28,18 +17,19 @@ process SPATYPER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def input_args = repeats && repeat_order ? "-r ${repeats} -o ${repeat_order}" : ""
"""
spaTyper \\
- $options.args \\
+ $args \\
$input_args \\
--fasta $fasta \\
--output ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(spaTyper --version 2>&1) | sed 's/^.*spaTyper //' )
+ "${task.process}":
+ spatyper: \$( echo \$(spaTyper --version 2>&1) | sed 's/^.*spaTyper //' )
END_VERSIONS
"""
}
diff --git a/modules/sratools/fasterqdump/functions.nf b/modules/sratools/fasterqdump/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/sratools/fasterqdump/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/sratools/fasterqdump/main.nf b/modules/sratools/fasterqdump/main.nf
index 08ef9045..73e3673d 100644
--- a/modules/sratools/fasterqdump/main.nf
+++ b/modules/sratools/fasterqdump/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SRATOOLS_FASTERQDUMP {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0 conda-forge::pigz=2.6' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
- } else {
- container 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
+ 'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
input:
tuple val(meta), path(sra)
@@ -26,6 +15,8 @@ process SRATOOLS_FASTERQDUMP {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
// Paired-end data extracted by fasterq-dump (--split-3 the default) always creates
// *_1.fastq *_2.fastq files but sometimes also an additional *.fastq file
@@ -39,19 +30,19 @@ process SRATOOLS_FASTERQDUMP {
fi
fasterq-dump \\
- ${options.args} \\
+ $args \\
--threads $task.cpus \\
${sra.name}
pigz \\
- ${options.args2} \\
+ $args2 \\
--no-name \\
--processes $task.cpus \\
*.fastq
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
+ "${task.process}":
+ sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
diff --git a/modules/sratools/prefetch/functions.nf b/modules/sratools/prefetch/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/sratools/prefetch/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/sratools/prefetch/main.nf b/modules/sratools/prefetch/main.nf
index 207d1e10..1e1eb802 100644
--- a/modules/sratools/prefetch/main.nf
+++ b/modules/sratools/prefetch/main.nf
@@ -1,23 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SRATOOLS_PREFETCH {
tag "$id"
label 'process_low'
label 'error_retry'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0'
- } else {
- container 'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
+ 'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
input:
tuple val(meta), val(id)
@@ -27,6 +16,7 @@ process SRATOOLS_PREFETCH {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
"""
eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
@@ -36,15 +26,15 @@ process SRATOOLS_PREFETCH {
fi
prefetch \\
- $options.args \\
+ $args \\
--progress \\
$id
vdb-validate $id
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+ "${task.process}":
+ sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
END_VERSIONS
"""
}
diff --git a/modules/staphopiasccmec/functions.nf b/modules/staphopiasccmec/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/staphopiasccmec/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/staphopiasccmec/main.nf b/modules/staphopiasccmec/main.nf
index 08def401..f33634ae 100644
--- a/modules/staphopiasccmec/main.nf
+++ b/modules/staphopiasccmec/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STAPHOPIASCCMEC {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::staphopia-sccmec=1.0.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/staphopia-sccmec:1.0.0--hdfd78af_0' :
+ 'quay.io/biocontainers/staphopia-sccmec:1.0.0--hdfd78af_0' }"
input:
tuple val(meta), path(fasta)
@@ -26,13 +15,14 @@ process STAPHOPIASCCMEC {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- staphopia-sccmec --assembly $fasta $options.args > ${prefix}.tsv
+ staphopia-sccmec --assembly $fasta $args > ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(staphopia-sccmec --version 2>&1 | sed 's/^.*staphopia-sccmec //')
+ "${task.process}":
+ staphopiasccmec: \$(staphopia-sccmec --version 2>&1 | sed 's/^.*staphopia-sccmec //')
END_VERSIONS
"""
}
diff --git a/modules/star/align/functions.nf b/modules/star/align/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/star/align/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf
index e0ccba8c..46023d3e 100644
--- a/modules/star/align/main.nf
+++ b/modules/star/align/main.nf
@@ -1,28 +1,20 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STAR_ALIGN {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? 'bioconda::star=2.7.9a' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0'
- } else {
- container 'quay.io/biocontainers/star:2.7.9a--h9ee0642_0'
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/star:2.7.9a--h9ee0642_0' :
+ 'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' }"
input:
tuple val(meta), path(reads)
path index
path gtf
+ val star_ignore_sjdbgtf
+ val seq_platform
+ val seq_center
output:
tuple val(meta), path('*d.out.bam') , emit: bam
@@ -39,12 +31,13 @@ process STAR_ALIGN {
tuple val(meta), path('*.out.junction') , optional:true, emit: junction
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
- def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
- def seq_platform = params.seq_platform ? "'PL:$params.seq_platform'" : ""
- def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
- def out_sam_type = (options.args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
- def mv_unsorted_bam = (options.args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
+ def seq_platform = seq_platform ? "'PL:$seq_platform'" : ""
+ def seq_center = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform "
+ def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted'
+ def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : ''
"""
STAR \\
--genomeDir $index \\
@@ -54,7 +47,7 @@ process STAR_ALIGN {
$out_sam_type \\
$ignore_gtf \\
$seq_center \\
- $options.args
+ $args
$mv_unsorted_bam
@@ -68,8 +61,8 @@ process STAR_ALIGN {
fi
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
+ "${task.process}":
+ star: \$(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS
"""
}
diff --git a/modules/star/genomegenerate/functions.nf b/modules/star/genomegenerate/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/star/genomegenerate/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/star/genomegenerate/main.nf b/modules/star/genomegenerate/main.nf
index c932fafe..ad32c0dd 100644
--- a/modules/star/genomegenerate/main.nf
+++ b/modules/star/genomegenerate/main.nf
@@ -1,23 +1,12 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STAR_GENOMEGENERATE {
tag "$fasta"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::star=2.7.9a bioconda::samtools=1.13 conda-forge::gawk=5.1.0" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0' :
+ 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:a7908dfb0485a80ca94e4d17b0ac991532e4e989-0' }"
input:
path fasta
@@ -28,9 +17,10 @@ process STAR_GENOMEGENERATE {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
+ def args_list = args.tokenize()
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
- def args = options.args.tokenize()
- if (args.contains('--genomeSAindexNbases')) {
+ if (args_list.contains('--genomeSAindexNbases')) {
"""
mkdir star
STAR \\
@@ -40,11 +30,11 @@ process STAR_GENOMEGENERATE {
--sjdbGTFfile $gtf \\
--runThreadN $task.cpus \\
$memory \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
+ "${task.process}":
+ star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
@@ -63,11 +53,11 @@ process STAR_GENOMEGENERATE {
--runThreadN $task.cpus \\
--genomeSAindexNbases \$NUM_BASES \\
$memory \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(STAR --version | sed -e "s/STAR_//g")
+ "${task.process}":
+ star: \$(STAR --version | sed -e "s/STAR_//g")
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
END_VERSIONS
diff --git a/modules/strelka/germline/functions.nf b/modules/strelka/germline/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/strelka/germline/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf
index 5e913c40..e991db67 100644
--- a/modules/strelka/germline/main.nf
+++ b/modules/strelka/germline/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STRELKA_GERMLINE {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
- } else {
- container "quay.io/biocontainers/strelka:2.9.10--0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--0' :
+ 'quay.io/biocontainers/strelka:2.9.10--0' }"
input:
tuple val(meta), path(input), path(input_index)
@@ -25,7 +14,6 @@ process STRELKA_GERMLINE {
path target_bed
path target_bed_tbi
-
output:
tuple val(meta), path("*variants.vcf.gz") , emit: vcf
tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi
@@ -34,14 +22,15 @@ process STRELKA_GERMLINE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def regions = target_bed ? "--exome --callRegions ${target_bed}" : ""
"""
configureStrelkaGermlineWorkflow.py \\
--bam $input \\
--referenceFasta $fasta \\
$regions \\
- $options.args \\
+ $args \\
--runDir strelka
python strelka/runWorkflow.py -m local -j $task.cpus
@@ -51,8 +40,8 @@ process STRELKA_GERMLINE {
mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( configureStrelkaGermlineWorkflow.py --version )
+ "${task.process}":
+ strelka: \$( configureStrelkaGermlineWorkflow.py --version )
END_VERSIONS
"""
}
diff --git a/modules/strelka/somatic/functions.nf b/modules/strelka/somatic/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/strelka/somatic/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/strelka/somatic/main.nf b/modules/strelka/somatic/main.nf
index 633b0a2c..fa138633 100644
--- a/modules/strelka/somatic/main.nf
+++ b/modules/strelka/somatic/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STRELKA_SOMATIC {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1"
- } else {
- container "quay.io/biocontainers/strelka:2.9.10--h9ee0642_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' :
+ 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }"
input:
tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi)
@@ -33,7 +22,8 @@ process STRELKA_SOMATIC {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : ""
def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : ""
"""
@@ -43,7 +33,7 @@ process STRELKA_SOMATIC {
--referenceFasta $fasta \\
$options_target_bed \\
$options_manta \\
- $options.args \\
+ $args \\
--runDir strelka
python strelka/runWorkflow.py -m local -j $task.cpus
@@ -54,8 +44,8 @@ process STRELKA_SOMATIC {
mv strelka/results/variants/somatic.snvs.vcf.gz.tbi ${prefix}.somatic_snvs.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( configureStrelkaSomaticWorkflow.py --version )
+ "${task.process}":
+ strelka: \$( configureStrelkaSomaticWorkflow.py --version )
END_VERSIONS
"""
}
diff --git a/modules/stringtie/merge/functions.nf b/modules/stringtie/merge/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/stringtie/merge/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf
index 371533bb..756dc6ec 100644
--- a/modules/stringtie/merge/main.nf
+++ b/modules/stringtie/merge/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STRINGTIE_MERGE {
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
// Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
- } else {
- container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
+ 'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
input:
path stringtie_gtf
@@ -27,6 +16,7 @@ process STRINGTIE_MERGE {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
stringtie \\
--merge $stringtie_gtf \\
@@ -34,8 +24,8 @@ process STRINGTIE_MERGE {
-o stringtie.merged.gtf
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(stringtie --version 2>&1)
+ "${task.process}":
+ stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/stringtie/stringtie/functions.nf b/modules/stringtie/stringtie/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/stringtie/stringtie/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf
index 3579e47c..4367a84d 100644
--- a/modules/stringtie/stringtie/main.nf
+++ b/modules/stringtie/stringtie/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process STRINGTIE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0"
- } else {
- container "quay.io/biocontainers/stringtie:2.1.7--h978d192_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
+ 'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
input:
tuple val(meta), path(bam)
@@ -30,7 +19,8 @@ process STRINGTIE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {
@@ -48,11 +38,11 @@ process STRINGTIE {
-C ${prefix}.coverage.gtf \\
-b ${prefix}.ballgown \\
-p $task.cpus \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(stringtie --version 2>&1)
+ "${task.process}":
+ stringtie: \$(stringtie --version 2>&1)
END_VERSIONS
"""
}
diff --git a/modules/subread/featurecounts/functions.nf b/modules/subread/featurecounts/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/subread/featurecounts/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf
index 0a0285db..43a7f8cd 100644
--- a/modules/subread/featurecounts/main.nf
+++ b/modules/subread/featurecounts/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process SUBREAD_FEATURECOUNTS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
- } else {
- container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' :
+ 'quay.io/biocontainers/subread:2.0.1--hed695b0_0' }"
input:
tuple val(meta), path(bams), path(annotation)
@@ -27,7 +16,8 @@ process SUBREAD_FEATURECOUNTS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def paired_end = meta.single_end ? '' : '-p'
def strandedness = 0
@@ -38,7 +28,7 @@ process SUBREAD_FEATURECOUNTS {
}
"""
featureCounts \\
- $options.args \\
+ $args \\
$paired_end \\
-T $task.cpus \\
-a $annotation \\
@@ -47,8 +37,8 @@ process SUBREAD_FEATURECOUNTS {
${bams.join(' ')}
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
+ "${task.process}":
+ subread: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
END_VERSIONS
"""
}
diff --git a/modules/tabix/bgzip/functions.nf b/modules/tabix/bgzip/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/tabix/bgzip/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/tabix/bgzip/main.nf b/modules/tabix/bgzip/main.nf
index 43726f17..13f9a942 100644
--- a/modules/tabix/bgzip/main.nf
+++ b/modules/tabix/bgzip/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TABIX_BGZIP {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
+ 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
input:
tuple val(meta), path(input)
@@ -26,13 +15,14 @@ process TABIX_BGZIP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- bgzip -c $options.args $input > ${prefix}.${input.getExtension()}.gz
+ bgzip -c $args $input > ${prefix}.${input.getExtension()}.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/tabix/bgziptabix/functions.nf b/modules/tabix/bgziptabix/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/tabix/bgziptabix/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf
index e44a7226..9a633d2e 100644
--- a/modules/tabix/bgziptabix/main.nf
+++ b/modules/tabix/bgziptabix/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TABIX_BGZIPTABIX {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
+ 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
input:
tuple val(meta), path(input)
@@ -26,14 +15,16 @@ process TABIX_BGZIPTABIX {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
- bgzip -c $options.args $input > ${prefix}.gz
- tabix $options.args2 ${prefix}.gz
+ bgzip -c $args $input > ${prefix}.gz
+ tabix $args2 ${prefix}.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/tabix/tabix/functions.nf b/modules/tabix/tabix/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/tabix/tabix/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf
index 1574c0b5..c721a554 100644
--- a/modules/tabix/tabix/main.nf
+++ b/modules/tabix/tabix/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TABIX_TABIX {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/tabix:1.11--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
+ 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
input:
tuple val(meta), path(tab)
@@ -26,12 +15,13 @@ process TABIX_TABIX {
path "versions.yml" , emit: versions
script:
+ def args = task.ext.args ?: ''
"""
- tabix $options.args $tab
+ tabix $args $tab
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+ "${task.process}":
+ tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/tbprofiler/profile/functions.nf b/modules/tbprofiler/profile/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/tbprofiler/profile/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/tbprofiler/profile/main.nf b/modules/tbprofiler/profile/main.nf
index afd78b05..3f6bffc3 100644
--- a/modules/tbprofiler/profile/main.nf
+++ b/modules/tbprofiler/profile/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TBPROFILER_PROFILE {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::tb-profiler=3.0.8" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0"
- } else {
- container "quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/tb-profiler:3.0.8--pypyh5e36f6f_0' :
+ 'quay.io/biocontainers/tb-profiler:3.0.8--pypyh5e36f6f_0' }"
input:
tuple val(meta), path(reads)
@@ -30,19 +19,20 @@ process TBPROFILER_PROFILE {
path "versions.yml" , emit: versions
script:
- prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def input_reads = meta.single_end ? "--read1 $reads" : "--read1 ${reads[0]} --read2 ${reads[1]}"
"""
tb-profiler \\
profile \\
- $options.args \\
+ $args \\
--prefix ${prefix} \\
--threads $task.cpus \\
$input_reads
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( echo \$(tb-profiler --version 2>&1) | sed 's/TBProfiler version //')
+ "${task.process}":
+ tbprofiler: \$( echo \$(tb-profiler --version 2>&1) | sed 's/TBProfiler version //')
END_VERSIONS
"""
}
diff --git a/modules/tiddit/cov/functions.nf b/modules/tiddit/cov/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/tiddit/cov/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/tiddit/cov/main.nf b/modules/tiddit/cov/main.nf
index a3a8a171..e9bb9b5d 100644
--- a/modules/tiddit/cov/main.nf
+++ b/modules/tiddit/cov/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TIDDIT_COV {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0"
- } else {
- container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
+ 'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
input:
tuple val(meta), path(bam)
@@ -25,25 +14,23 @@ process TIDDIT_COV {
output:
tuple val(meta), path("*.tab"), optional: true, emit: cov
tuple val(meta), path("*.wig"), optional: true, emit: wig
-
path "versions.yml" , emit: versions
script:
- def software = getSoftwareName(task.process)
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def reference = fasta ? "--ref $fasta" : ""
"""
tiddit \\
--cov \\
-o $prefix \\
- $options.args \\
+ $args \\
--bam $bam \\
$reference
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+ "${task.process}":
+ tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/tiddit/sv/functions.nf b/modules/tiddit/sv/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/tiddit/sv/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index e262221a..83a46f82 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TIDDIT_SV {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::tiddit=2.12.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0"
- } else {
- container "quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/tiddit:2.12.1--py38h1773678_0' :
+ 'quay.io/biocontainers/tiddit:2.12.1--py38h1773678_0' }"
input:
tuple val(meta), path(bam)
@@ -30,19 +19,20 @@ process TIDDIT_SV {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
"""
tiddit \\
--sv \\
- $options.args \\
+ $args \\
--bam $bam \\
$reference \\
-o $prefix
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
+ "${task.process}":
+ tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*TIDDIT-//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/trimgalore/functions.nf b/modules/trimgalore/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/trimgalore/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf
index 8e77f1f7..86761ad8 100644
--- a/modules/trimgalore/main.nf
+++ b/modules/trimgalore/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process TRIMGALORE {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0"
- } else {
- container "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' :
+ 'quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0' }"
input:
tuple val(meta), path(reads)
@@ -30,6 +19,7 @@ process TRIMGALORE {
tuple val(meta), path("*.zip") , emit: zip optional true
script:
+ def args = task.ext.args ?: ''
// Calculate number of --cores for TrimGalore based on value of task.cpus
// See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
// See: https://github.com/nf-core/atacseq/pull/65
@@ -48,20 +38,20 @@ process TRIMGALORE {
def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
// Added soft-links to original fastqs for consistent naming in MultiQC
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
trim_galore \\
- $options.args \\
+ $args \\
--cores $cores \\
--gzip \\
$c_r1 \\
$tpc_r1 \\
${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
+ "${task.process}":
+ trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
cutadapt: \$(cutadapt --version)
END_VERSIONS
"""
@@ -70,7 +60,7 @@ process TRIMGALORE {
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
trim_galore \\
- $options.args \\
+ $args \\
--cores $cores \\
--paired \\
--gzip \\
@@ -81,8 +71,8 @@ process TRIMGALORE {
${prefix}_1.fastq.gz \\
${prefix}_2.fastq.gz
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
+ "${task.process}":
+ trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
cutadapt: \$(cutadapt --version)
END_VERSIONS
"""
diff --git a/modules/ucsc/bed12tobigbed/functions.nf b/modules/ucsc/bed12tobigbed/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ucsc/bed12tobigbed/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ucsc/bed12tobigbed/main.nf b/modules/ucsc/bed12tobigbed/main.nf
index 81f39a6f..937eabd6 100644
--- a/modules/ucsc/bed12tobigbed/main.nf
+++ b/modules/ucsc/bed12tobigbed/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '377'
+def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_BED12TOBIGBED {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--h446ed27_1"
- } else {
- container "quay.io/biocontainers/ucsc-bedtobigbed:377--h446ed27_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--h446ed27_1' :
+ 'quay.io/biocontainers/ucsc-bedtobigbed:377--h446ed27_1' }"
input:
tuple val(meta), path(bed)
@@ -29,7 +18,8 @@ process UCSC_BED12TOBIGBED {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
bedToBigBed \\
$bed \\
@@ -37,8 +27,8 @@ process UCSC_BED12TOBIGBED {
${prefix}.bigBed
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ ucsc: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/ucsc/bedclip/functions.nf b/modules/ucsc/bedclip/functions.nf
deleted file mode 100755
index 85628ee0..00000000
--- a/modules/ucsc/bedclip/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ucsc/bedclip/main.nf b/modules/ucsc/bedclip/main.nf
index 5fbc2b3b..1d46342c 100755
--- a/modules/ucsc/bedclip/main.nf
+++ b/modules/ucsc/bedclip/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '377'
+def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_BEDCLIP {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2"
- } else {
- container "quay.io/biocontainers/ucsc-bedclip:377--h0b8a92a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' :
+ 'quay.io/biocontainers/ucsc-bedclip:377--h0b8a92a_2' }"
input:
tuple val(meta), path(bedgraph)
@@ -29,7 +18,8 @@ process UCSC_BEDCLIP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
bedClip \\
$bedgraph \\
@@ -37,8 +27,8 @@ process UCSC_BEDCLIP {
${prefix}.bedGraph
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ ucsc: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/ucsc/bedgraphtobigwig/functions.nf b/modules/ucsc/bedgraphtobigwig/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ucsc/bedgraphtobigwig/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ucsc/bedgraphtobigwig/main.nf b/modules/ucsc/bedgraphtobigwig/main.nf
index f55cdb07..e18b41bc 100644
--- a/modules/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/ucsc/bedgraphtobigwig/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '377'
+def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_BEDGRAPHTOBIGWIG {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
- } else {
- container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' :
+ 'quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1' }"
input:
tuple val(meta), path(bedgraph)
@@ -29,7 +18,8 @@ process UCSC_BEDGRAPHTOBIGWIG {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
bedGraphToBigWig \\
$bedgraph \\
@@ -37,8 +27,8 @@ process UCSC_BEDGRAPHTOBIGWIG {
${prefix}.bigWig
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ ucsc: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/ucsc/bigwigaverageoverbed/functions.nf b/modules/ucsc/bigwigaverageoverbed/functions.nf
deleted file mode 100755
index 85628ee0..00000000
--- a/modules/ucsc/bigwigaverageoverbed/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ucsc/bigwigaverageoverbed/main.nf b/modules/ucsc/bigwigaverageoverbed/main.nf
index 72491443..8c6f1178 100644
--- a/modules/ucsc/bigwigaverageoverbed/main.nf
+++ b/modules/ucsc/bigwigaverageoverbed/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '377'
+def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_BIGWIGAVERAGEOVERBED {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2"
- } else {
- container "quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h0b8a92a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' :
+ 'quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' }"
input:
tuple val(meta), path(bed)
@@ -29,18 +18,19 @@ process UCSC_BIGWIGAVERAGEOVERBED {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ // BUG: bigWigAverageOverBed cannot handle ensembl seqlevels style
"""
- # there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style.
bigWigAverageOverBed \\
- $options.args \\
+ $args \\
$bigwig \\
$bed \\
${prefix}.tab
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ ucsc: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/ucsc/liftover/functions.nf b/modules/ucsc/liftover/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ucsc/liftover/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ucsc/liftover/main.nf b/modules/ucsc/liftover/main.nf
index 3739a1e5..1c667262 100644
--- a/modules/ucsc/liftover/main.nf
+++ b/modules/ucsc/liftover/main.nf
@@ -1,24 +1,13 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '377'
+def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_LIFTOVER {
tag "$meta.id"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3"
- } else {
- container "quay.io/biocontainers/ucsc-liftover:377--h0b8a92a_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' :
+ 'quay.io/biocontainers/ucsc-liftover:377--h0b8a92a_3' }"
input:
tuple val(meta), path(bed)
@@ -30,19 +19,20 @@ process UCSC_LIFTOVER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
liftOver \\
- $options.args \
+ $args \
$bed \\
$chain \\
${prefix}.lifted.bed \\
${prefix}.unlifted.bed
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo "$VERSION")
+ "${task.process}":
+ ucsc: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/ucsc/wigtobigwig/functions.nf b/modules/ucsc/wigtobigwig/functions.nf
deleted file mode 100755
index 85628ee0..00000000
--- a/modules/ucsc/wigtobigwig/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf
index d03a2c4a..4c596c9a 100644
--- a/modules/ucsc/wigtobigwig/main.nf
+++ b/modules/ucsc/wigtobigwig/main.nf
@@ -1,45 +1,34 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '377' // No version information printed
+def VERSION = '377' // Version information not provided by tool on CLI
process UCSC_WIGTOBIGWIG {
tag '$wig'
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2"
- } else {
- container "quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' :
+ 'quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2' }"
input:
path wig
- path chromsizes
+ path sizes
output:
- path "*.bw" , emit: bw
- path "versions.yml" , emit: versions
+ path "*.bw" , emit: bw
+ path "versions.yml", emit: versions
script:
-
+ def args = task.ext.args ?: ''
"""
wigToBigWig \\
- $options.args \\
+ $args \\
$wig \\
- $chromsizes \\
+ $sizes \\
${wig.getSimpleName()}.bw
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo "$VERSION")
+ "${task.process}":
+ ucsc: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/ultra/pipeline/functions.nf b/modules/ultra/pipeline/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/ultra/pipeline/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/ultra/pipeline/main.nf b/modules/ultra/pipeline/main.nf
index b61518e6..5df34121 100644
--- a/modules/ultra/pipeline/main.nf
+++ b/modules/ultra/pipeline/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process ULTRA_PIPELINE {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::ultra_bioinformatics=0.0.4.1" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
- } else {
- container "quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' :
+ 'quay.io/biocontainers/ultra_bioinformatics:0.0.4.1--pyh5e36f6f_0' }"
input:
tuple val(meta), path(reads)
@@ -28,21 +17,22 @@ process ULTRA_PIPELINE {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
uLTRA \\
pipeline \\
--t $task.cpus \\
--prefix $prefix \\
- $options.args \\
+ $args \\
$genome \\
$gtf \\
$reads \\
./
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$( uLTRA --version|sed 's/uLTRA //g' )
+ "${task.process}":
+ ultra: \$( uLTRA --version|sed 's/uLTRA //g' )
END_VERSIONS
"""
}
diff --git a/modules/umitools/dedup/functions.nf b/modules/umitools/dedup/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/umitools/dedup/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/umitools/dedup/main.nf b/modules/umitools/dedup/main.nf
index 0ec9741b..287bb8c2 100644
--- a/modules/umitools/dedup/main.nf
+++ b/modules/umitools/dedup/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process UMITOOLS_DEDUP {
tag "$meta.id"
label "process_medium"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
- } else {
- container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' :
+ 'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }"
input:
tuple val(meta), path(bam), path(bai)
@@ -26,18 +15,19 @@ process UMITOOLS_DEDUP {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def paired = meta.single_end ? "" : "--paired"
"""
umi_tools dedup \\
-I $bam \\
-S ${prefix}.bam \\
$paired \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+ "${task.process}":
+ umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
}
diff --git a/modules/umitools/extract/functions.nf b/modules/umitools/extract/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/umitools/extract/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/umitools/extract/main.nf b/modules/umitools/extract/main.nf
index d90a3ba8..3c2402e2 100644
--- a/modules/umitools/extract/main.nf
+++ b/modules/umitools/extract/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process UMITOOLS_EXTRACT {
tag "$meta.id"
label "process_low"
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
- } else {
- container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' :
+ 'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }"
input:
tuple val(meta), path(reads)
@@ -27,19 +16,20 @@ process UMITOOLS_EXTRACT {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
umi_tools \\
extract \\
-I $reads \\
-S ${prefix}.umi_extract.fastq.gz \\
- $options.args \\
+ $args \\
> ${prefix}.umi_extract.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+ "${task.process}":
+ umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
} else {
@@ -50,12 +40,12 @@ process UMITOOLS_EXTRACT {
--read2-in=${reads[1]} \\
-S ${prefix}.umi_extract_1.fastq.gz \\
--read2-out=${prefix}.umi_extract_2.fastq.gz \\
- $options.args \\
+ $args \\
> ${prefix}.umi_extract.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
+ "${task.process}":
+ umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
END_VERSIONS
"""
}
diff --git a/modules/unicycler/functions.nf b/modules/unicycler/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/unicycler/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/unicycler/main.nf b/modules/unicycler/main.nf
index 3629d730..14319dc1 100644
--- a/modules/unicycler/main.nf
+++ b/modules/unicycler/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process UNICYCLER {
tag "$meta.id"
label 'process_high'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? 'bioconda::unicycler=0.4.8' : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3"
- } else {
- container "quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' :
+ 'quay.io/biocontainers/unicycler:0.4.8--py38h8162308_3' }"
input:
tuple val(meta), path(shortreads), path(longreads)
@@ -28,13 +17,14 @@ process UNICYCLER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def short_reads = shortreads ? ( meta.single_end ? "-s $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" ) : ""
def long_reads = longreads ? "-l $longreads" : ""
"""
unicycler \\
--threads $task.cpus \\
- $options.args \\
+ $args \\
$short_reads \\
$long_reads \\
--out ./
@@ -46,8 +36,8 @@ process UNICYCLER {
mv unicycler.log ${prefix}.unicycler.log
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
+ "${task.process}":
+ unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/untar/functions.nf b/modules/untar/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/untar/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/untar/main.nf b/modules/untar/main.nf
index efb9d825..6d1996e7 100644
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process UNTAR {
tag "$archive"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
- } else {
- container "biocontainers/biocontainers:v1.2.0_cv1"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
+ 'biocontainers/biocontainers:v1.2.0_cv1' }"
input:
path archive
@@ -26,16 +15,19 @@ process UNTAR {
path "versions.yml", emit: versions
script:
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
untar = archive.toString() - '.tar.gz'
"""
tar \\
-xzvf \\
- $options.args \\
- $archive
+ $args \\
+ $archive \\
+ $args2 \\
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
+ "${task.process}":
+ untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}
diff --git a/modules/unzip/functions.nf b/modules/unzip/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/unzip/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/unzip/main.nf b/modules/unzip/main.nf
index f39e75e8..294ac0b0 100644
--- a/modules/unzip/main.nf
+++ b/modules/unzip/main.nf
@@ -1,23 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process UNZIP {
tag "$archive"
label 'process_low'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
-
conda (params.enable_conda ? "bioconda::p7zip=15.09" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4"
- } else {
- container "quay.io/biocontainers/p7zip:15.09--h2d50403_4"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/p7zip:15.09--h2d50403_4' :
+ 'quay.io/biocontainers/p7zip:15.09--h2d50403_4' }"
input:
path archive
@@ -27,17 +15,17 @@ process UNZIP {
path "versions.yml" , emit: versions
script:
-
+ def args = task.ext.args ?: ''
if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
"""
7za \\
e \\
-o"${archive.baseName}"/ \\
- $options.args \\
+ $args \\
$archive
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
+ "${task.process}":
7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//')
END_VERSIONS
"""
diff --git a/modules/variantbam/functions.nf b/modules/variantbam/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/variantbam/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/variantbam/main.nf b/modules/variantbam/main.nf
index e73b8bf1..3d354016 100644
--- a/modules/variantbam/main.nf
+++ b/modules/variantbam/main.nf
@@ -1,43 +1,33 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
-def VERSION = '1.4.4a'
+def VERSION = '1.4.4a' // Version information not provided by tool on CLI
process VARIANTBAM {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5"
- } else {
- container "quay.io/biocontainers/variantbam:1.4.4a--h7d7f7ad_5"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' :
+ 'quay.io/biocontainers/variantbam:1.4.4a--h7d7f7ad_5' }"
input:
tuple val(meta), path(bam)
output:
- tuple val(meta), path("*.bam") , emit: bam
- path "versions.yml" , emit: versions
+ tuple val(meta), path("*.bam"), emit: bam
+ path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
"""
variant \\
$bam \\
-o ${prefix}.bam \\
- $options.args
+ $args
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo $VERSION)
+ "${task.process}":
+ variantbam: $VERSION
END_VERSIONS
"""
}
diff --git a/modules/vcftools/functions.nf b/modules/vcftools/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/vcftools/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/vcftools/main.nf b/modules/vcftools/main.nf
index 768d5a23..62fff0cf 100644
--- a/modules/vcftools/main.nf
+++ b/modules/vcftools/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process VCFTOOLS {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4"
- } else {
- container "quay.io/biocontainers/vcftools:0.1.16--he513fc3_4"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/vcftools:0.1.16--he513fc3_4' :
+ 'quay.io/biocontainers/vcftools:0.1.16--he513fc3_4' }"
input:
// Owing to the nature of vcftools we here provide solutions to working with optional bed files and optional
@@ -93,22 +82,23 @@ process VCFTOOLS {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
- def args = options.args.tokenize()
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+ def args_list = args.tokenize()
- def bed_arg = (options.args.contains('--bed')) ? "--bed ${bed}" :
- (options.args.contains('--exclude-bed')) ? "--exclude-bed ${bed}" :
- (options.args.contains('--hapcount')) ? "--hapcount ${bed}" : ''
- args.removeIf { it.contains('--bed') }
- args.removeIf { it.contains('--exclude-bed') }
- args.removeIf { it.contains('--hapcount') }
+ def bed_arg = (args.contains('--bed')) ? "--bed ${bed}" :
+ (args.contains('--exclude-bed')) ? "--exclude-bed ${bed}" :
+ (args.contains('--hapcount')) ? "--hapcount ${bed}" : ''
+ args_list.removeIf { it.contains('--bed') }
+ args_list.removeIf { it.contains('--exclude-bed') }
+ args_list.removeIf { it.contains('--hapcount') }
- def diff_variant_arg = (options.args.contains('--diff')) ? "--diff ${diff_variant_file}" :
- (options.args.contains('--gzdiff')) ? "--gzdiff ${diff_variant_file}" :
- (options.args.contains('--diff-bcf')) ? "--diff-bcf ${diff_variant_file}" : ''
- args.removeIf { it.contains('--diff') }
- args.removeIf { it.contains('--gzdiff') }
- args.removeIf { it.contains('--diff-bcf') }
+ def diff_variant_arg = (args.contains('--diff')) ? "--diff ${diff_variant_file}" :
+ (args.contains('--gzdiff')) ? "--gzdiff ${diff_variant_file}" :
+ (args.contains('--diff-bcf')) ? "--diff-bcf ${diff_variant_file}" : ''
+ args_list.removeIf { it.contains('--diff') }
+ args_list.removeIf { it.contains('--gzdiff') }
+ args_list.removeIf { it.contains('--diff-bcf') }
def input_file = ("$variant_file".endsWith(".vcf")) ? "--vcf ${variant_file}" :
("$variant_file".endsWith(".vcf.gz")) ? "--gzvcf ${variant_file}" :
@@ -118,13 +108,13 @@ process VCFTOOLS {
vcftools \\
$input_file \\
--out $prefix \\
- ${args.join(' ')} \\
+ ${args_list.join(' ')} \\
$bed_arg \\
$diff_variant_arg
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
+ "${task.process}":
+ vcftools: \$(echo \$(vcftools --version 2>&1) | sed 's/^.*VCFtools (//;s/).*//')
END_VERSIONS
"""
}
diff --git a/modules/yara/index/functions.nf b/modules/yara/index/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/yara/index/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/yara/index/main.nf b/modules/yara/index/main.nf
index 51ae8a32..77122c78 100644
--- a/modules/yara/index/main.nf
+++ b/modules/yara/index/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process YARA_INDEX {
tag "$fasta"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::yara=1.0.2" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/yara:1.0.2--2"
- } else {
- container "quay.io/biocontainers/yara:1.0.2--2"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/yara:1.0.2--2' :
+ 'quay.io/biocontainers/yara:1.0.2--2' }"
input:
path fasta
@@ -26,6 +15,7 @@ process YARA_INDEX {
path "versions.yml", emit: versions
script:
+ def args = task.ext.args ?: ''
"""
mkdir yara
@@ -38,8 +28,8 @@ process YARA_INDEX {
cp $fasta yara/yara.fasta
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(yara_indexer --version 2>&1) | sed 's/^.*yara_indexer version: //; s/ .*\$//')
+ "${task.process}":
+ yara: \$(echo \$(yara_indexer --version 2>&1) | sed 's/^.*yara_indexer version: //; s/ .*\$//')
END_VERSIONS
"""
}
diff --git a/modules/yara/mapper/functions.nf b/modules/yara/mapper/functions.nf
deleted file mode 100644
index 85628ee0..00000000
--- a/modules/yara/mapper/functions.nf
+++ /dev/null
@@ -1,78 +0,0 @@
-//
-// Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
- return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Extract name of module from process name using $task.process
-//
-def getProcessName(task_process) {
- return task_process.tokenize(':')[-1]
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
- def Map options = [:]
- options.args = args.args ?: ''
- options.args2 = args.args2 ?: ''
- options.args3 = args.args3 ?: ''
- options.publish_by_meta = args.publish_by_meta ?: []
- options.publish_dir = args.publish_dir ?: ''
- options.publish_files = args.publish_files
- options.suffix = args.suffix ?: ''
- return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
- def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
- paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
- return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
- def ioptions = initOptions(args.options)
- def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-
- // Do not publish versions.yml unless running from pytest workflow
- if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
- return null
- }
- if (ioptions.publish_by_meta) {
- def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
- for (key in key_list) {
- if (args.meta && key instanceof String) {
- def path = key
- if (args.meta.containsKey(key)) {
- path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
- }
- path = path instanceof String ? path : ''
- path_list.add(path)
- }
- }
- }
- if (ioptions.publish_files instanceof Map) {
- for (ext in ioptions.publish_files) {
- if (args.filename.endsWith(ext.key)) {
- def ext_list = path_list.collect()
- ext_list.add(ext.value)
- return "${getPathFromList(ext_list)}/$args.filename"
- }
- }
- } else if (ioptions.publish_files == null) {
- return "${getPathFromList(path_list)}/$args.filename"
- }
-}
diff --git a/modules/yara/mapper/main.nf b/modules/yara/mapper/main.nf
index 3d69674c..6e7f433b 100644
--- a/modules/yara/mapper/main.nf
+++ b/modules/yara/mapper/main.nf
@@ -1,22 +1,11 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
-
-params.options = [:]
-options = initOptions(params.options)
-
process YARA_MAPPER {
tag "$meta.id"
label 'process_medium'
- publishDir "${params.outdir}",
- mode: params.publish_dir_mode,
- saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
- if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container "https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0"
- } else {
- container "quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0"
- }
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' :
+ 'quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0' }"
input:
tuple val(meta), path(reads)
@@ -27,27 +16,28 @@ process YARA_MAPPER {
path "versions.yml" , emit: versions
script:
- def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
if (meta.single_end) {
"""
yara_mapper \\
- $options.args \\
+ $args \\
-t $task.cpus \\
-f bam \\
${index}/yara \\
$reads | samtools view -@ $task.cpus -hb -F4 > ${prefix}.mapped.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
+ "${task.process}":
+ yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
} else {
"""
yara_mapper \\
- $options.args \\
- -t ${task.cpus} \\
+ $args \\
+ -t $task.cpus \\
-f bam \\
${index}/yara \\
${reads[0]} \\
@@ -57,8 +47,8 @@ process YARA_MAPPER {
samtools view -@ $task.cpus -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
cat <<-END_VERSIONS > versions.yml
- ${getProcessName(task.process)}:
- ${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
+ "${task.process}":
+ yara: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index cd22dde8..741edf5e 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -6,9 +6,9 @@ params {
}
process {
- cpus = 2
- memory = 3.GB
- time = 2.h
+ cpus = 2
+ memory = 3.GB
+ time = 2.h
}
if ("$PROFILE" == "singularity") {
@@ -28,5 +28,5 @@ conda { createTimeout = "120 min" }
includeConfig 'test_data.config'
manifest {
- nextflowVersion = '!>=21.04.0'
+ nextflowVersion = '!>=21.10.3'
}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index d68d64d0..aa59b7c9 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -305,7 +305,7 @@ cooler/digest:
cooler/cload:
- modules/cooler/cload/**
- tests/modules/cooler/cload/**
-
+
cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
@@ -349,7 +349,7 @@ dastool/dastool:
dastool/scaffolds2bin:
- modules/dastool/scaffolds2bin/**
- tests/modules/dastool/scaffolds2bin/**
-
+
dedup:
- modules/dedup/**
- tests/modules/dedup/**
@@ -490,7 +490,7 @@ gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
-gatk4/calculatecontamination: &gatk4_calculatecontamination
+gatk4/calculatecontamination: #&gatk4_calculatecontamination
- modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/**
@@ -498,7 +498,7 @@ gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/**
-gatk4/createsomaticpanelofnormals: &gatk4_createsomaticpanelofnormals
+gatk4/createsomaticpanelofnormals: #&gatk4_createsomaticpanelofnormals
- modules/gatk4/createsomaticpanelofnormals/**
- tests/modules/gatk4/createsomaticpanelofnormals/**
@@ -510,11 +510,11 @@ gatk4/fastqtosam:
- modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/**
-gatk4/filtermutectcalls: &gatk4_filtermutectcalls
+gatk4/filtermutectcalls: #&gatk4_filtermutectcalls
- modules/gatk4/filtermutectcalls/**
- tests/modules/gatk4/filtermutectcalls/**
-gatk4/genomicsdbimport: &gatk4_genomicsdbimport
+gatk4/genomicsdbimport: #&gatk4_genomicsdbimport
- modules/gatk4/genomicsdbimport/**
- tests/modules/gatk4/genomicsdbimport/**
@@ -522,7 +522,7 @@ gatk4/genotypegvcfs:
- modules/gatk4/genotypegvcfs/**
- tests/modules/gatk4/genotypegvcfs/**
-gatk4/getpileupsummaries: &gatk4_getpileupsummaries
+gatk4/getpileupsummaries: #&gatk4_getpileupsummaries
- modules/gatk4/getpileupsummaries/**
- tests/modules/gatk4/getpileupsummaries/**
@@ -538,7 +538,7 @@ gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
-gatk4/learnreadorientationmodel: &gatk4_learnreadorientationmodel
+gatk4/learnreadorientationmodel: #&gatk4_learnreadorientationmodel
- modules/gatk4/learnreadorientationmodel/**
- tests/modules/gatk4/learnreadorientationmodel/**
@@ -554,7 +554,7 @@ gatk4/mergevcfs:
- modules/gatk4/mergevcfs/**
- tests/modules/gatk4/mergevcfs/**
-gatk4/mutect2: &gatk4_mutect2
+gatk4/mutect2: #&gatk4_mutect2
- modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/**
@@ -746,13 +746,13 @@ kraken2/kraken2:
- modules/untar/**
- tests/modules/kraken2/kraken2/**
-kronatools/kronadb:
- - modules/kronatools/kronadb/**
- - tests/modules/kronatools/kronadb/**
+krona/kronadb:
+ - modules/krona/kronadb/**
+ - tests/modules/krona/kronadb/**
-kronatools/ktimporttaxonomy:
- - modules/kronatools/ktimporttaxonomy/**
- - tests/modules/kronatools/ktimporttaxonomy/**
+krona/ktimporttaxonomy:
+ - modules/krona/ktimporttaxonomy/**
+ - tests/modules/krona/ktimporttaxonomy/**
last/dotplot:
- modules/last/dotplot/**
@@ -1063,6 +1063,10 @@ plink/vcf:
- modules/plink/vcf/**
- tests/modules/plink/vcf/**
+plink2/vcf:
+ - modules/plink2/vcf/**
+ - tests/modules/plink2/vcf/**
+
pmdtools/filter:
- modules/pmdtools/filter/**
- tests/modules/pmdtools/filter/**
@@ -1211,7 +1215,7 @@ samtools/idxstats:
- modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/**
-samtools/index: &samtools_index
+samtools/index: #&samtools_index
- modules/samtools/index/**
- tests/modules/samtools/index/**
@@ -1223,7 +1227,7 @@ samtools/mpileup:
- modules/samtools/mpileup/**
- tests/modules/samtools/mpileup/**
-samtools/sort: &samtools_sort
+samtools/sort: #&samtools_sort
- modules/samtools/sort/**
- tests/modules/samtools/sort/**
@@ -1246,7 +1250,7 @@ seacr/callpeak:
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
-
+
seqsero2:
- modules/seqsero2/**
- tests/modules/seqsero2/**
@@ -1299,11 +1303,11 @@ spatyper:
- modules/spatyper/**
- tests/modules/spatyper/**
-sratools/fasterqdump: &sratools_fasterqdump
+sratools/fasterqdump: #&sratools_fasterqdump
- modules/sratools/fasterqdump/**
- tests/modules/sratools/fasterqdump/**
-sratools/prefetch: &sratools_prefetch
+sratools/prefetch: #&sratools_prefetch
- modules/sratools/prefetch/**
- tests/modules/sratools/prefetch/**
@@ -1423,47 +1427,47 @@ yara/mapper:
- modules/yara/mapper/**
- tests/modules/yara/mapper/**
-subworkflows/bam_stats_samtools: &subworkflows_bam_stats_samtools
- - subworkflows/nf-core/bam_stats_samtools/**
- - tests/subworkflows/nf-core/bam_stats_samtools/**
+# subworkflows/bam_stats_samtools: &subworkflows_bam_stats_samtools
+# - subworkflows/nf-core/bam_stats_samtools/**
+# - tests/subworkflows/nf-core/bam_stats_samtools/**
-subworkflows/bam_sort_samtools: &subworkflows_bam_sort_samtools
- - subworkflows/nf-core/bam_sort_samtools/**
- - tests/subworkflows/nf-core/bam_sort_samtools/**
- - *samtools_sort
- - *samtools_index
- - *subworkflows_bam_stats_samtools
+# subworkflows/bam_sort_samtools: &subworkflows_bam_sort_samtools
+# - subworkflows/nf-core/bam_sort_samtools/**
+# - tests/subworkflows/nf-core/bam_sort_samtools/**
+# - *samtools_sort
+# - *samtools_index
+# - *subworkflows_bam_stats_samtools
-subworkflows/align_bowtie2:
- - subworkflows/nf-core/align_bowtie2/**
- - tests/subworkflows/nf-core/align_bowtie2/**
- - *subworkflows_bam_sort_samtools
+# subworkflows/align_bowtie2:
+# - subworkflows/nf-core/align_bowtie2/**
+# - tests/subworkflows/nf-core/align_bowtie2/**
+# - *subworkflows_bam_sort_samtools
-subworkflows/sra_fastq:
- - subworkflows/nf-core/sra_fastq/**
- - tests/subworkflows/nf-core/sra_fastq/**
- - *sratools_fasterqdump
- - *sratools_prefetch
+# subworkflows/sra_fastq:
+# - subworkflows/nf-core/sra_fastq/**
+# - tests/subworkflows/nf-core/sra_fastq/**
+# - *sratools_fasterqdump
+# - *sratools_prefetch
-subworkflows/gatk_create_som_pon:
- - subworkflows/nf-core/gatk_create_som_pon/**
- - tests/subworkflows/nf-core/gatk_create_som_pon/**
- - *gatk4_genomicsdbimport
- - *gatk4_createsomaticpanelofnormals
+# subworkflows/gatk_create_som_pon:
+# - subworkflows/nf-core/gatk_create_som_pon/**
+# - tests/subworkflows/nf-core/gatk_create_som_pon/**
+# - *gatk4_genomicsdbimport
+# - *gatk4_createsomaticpanelofnormals
-subworkflows/gatk_tumor_normal_somatic_variant_calling:
- - subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
- - tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
- - *gatk4_mutect2
- - *gatk4_learnreadorientationmodel
- - *gatk4_getpileupsummaries
- - *gatk4_calculatecontamination
- - *gatk4_filtermutectcalls
-
-subworkflows/gatk_tumor_only_somatic_variant_calling:
- - subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
- - tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
- - *gatk4_mutect2
- - *gatk4_getpileupsummaries
- - *gatk4_calculatecontamination
- - *gatk4_filtermutectcalls
+# subworkflows/gatk_tumor_normal_somatic_variant_calling:
+# - subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
+# - tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/**
+# - *gatk4_mutect2
+# - *gatk4_learnreadorientationmodel
+# - *gatk4_getpileupsummaries
+# - *gatk4_calculatecontamination
+# - *gatk4_filtermutectcalls
+
+# subworkflows/gatk_tumor_only_somatic_variant_calling:
+# - subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
+# - tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/**
+# - *gatk4_mutect2
+# - *gatk4_getpileupsummaries
+# - *gatk4_calculatecontamination
+# - *gatk4_filtermutectcalls
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 0c7ce2fc..31e17618 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -221,8 +221,8 @@ params {
test_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
test2_narrowpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
- test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_1.fastq.gz"
- test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test.10x_2.fastq.gz"
+ test_10x_1_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
+ test_10x_2_fastq_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
test_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
test2_yak = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
@@ -252,6 +252,56 @@ params {
filelist = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
}
}
+ 'bacteroides_fragilis' {
+ 'genome' {
+ genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
+ genome_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
+ }
+ 'illumina' {
+ test1_contigs_fa_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
+ test1_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
+ test1_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
+ test2_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
+ test2_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
+ test1_paired_end_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.bam"
+ test1_paired_end_sorted_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
+ test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
+ test2_paired_end_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.bam"
+ test2_paired_end_sorted_bam = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
+ test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
+ }
+ 'nanopore' {
+ test_fastq_gz = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
+ overlap_paf = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/nanopore/overlap.paf"
+ }
+ }
+ 'candidatus_portiera_aleyrodidarum' {
+ 'genome' {
+ genome_fasta = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta"
+ genome_sizes = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.sizes"
+ genome_aln_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.gz"
+ genome_aln_nwk = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.aln.nwk"
+ proteome_fasta = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/proteome.fasta"
+ test1_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test1.gff"
+ test2_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test2.gff"
+ test3_gff = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/gff/test3.gff"
+ }
+ 'illumina' {
+ test_1_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fasta/test_1.fastq.gz"
+ test_2_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_2.fastq.gz"
+ test_se_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/illumina/fastq/test_se.fastq.gz"
+ }
+ 'nanopore' {
+ test_fastq_gz = "${test_data_dir}/genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz"
+ }
+ }
+ 'haemophilus_influenzae' {
+ 'genome' {
+ genome_fna_gz = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz"
+ genome_aln_gz = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.gz"
+ genome_aln_nwk = "${test_data_dir}/genomics/prokaryotes/haemophilus_influenzae/genome/genome.aln.nwk"
+ }
+ }
'generic' {
'csv' {
test_csv = "${test_data_dir}/generic/csv/test.csv"
@@ -282,28 +332,5 @@ params {
}
}
- 'bacteroides_fragilis'{
- 'genome' {
- genome_fna_gz = "${test_data_dir}/genomics/bacteroides_fragilis/genome/genome.fna.gz"
- genome_paf = "${test_data_dir}/genomics/bacteroides_fragilis/genome/genome.paf"
- }
- 'illumina' {
- test1_contigs_fa_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"
- test1_1_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz"
- test1_2_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test1_2.fastq.gz"
- test2_1_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test2_1.fastq.gz"
- test2_2_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/fastq/test2_2.fastq.gz"
- test1_paired_end_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.bam"
- test1_paired_end_sorted_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.sorted.bam"
- test1_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test1.sorted.bam.bai"
- test2_paired_end_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.bam"
- test2_paired_end_sorted_bam = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.sorted.bam"
- test2_paired_end_sorted_bam_bai = "${test_data_dir}/genomics/bacteroides_fragilis/illumina/bam/test2.sorted.bam.bai"
- }
- 'nanopore' {
- test_fastq_gz = "${test_data_dir}/genomics/bacteroides_fragilis/nanopore/fastq/test.fastq.gz"
- overlap_paf = "${test_data_dir}/genomics/bacteroides_fragilis/nanopore/overlap.paf"
- }
- }
}
}
diff --git a/tests/modules/abacas/main.nf b/tests/modules/abacas/main.nf
index dc58ed61..542a67af 100644
--- a/tests/modules/abacas/main.nf
+++ b/tests/modules/abacas/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ABACAS } from '../../../modules/abacas/main.nf' addParams ( options: ['args' : '-m -p nucmer'] )
+include { ABACAS } from '../../../modules/abacas/main.nf'
workflow test_abacas {
diff --git a/tests/modules/abacas/nextflow.config b/tests/modules/abacas/nextflow.config
new file mode 100644
index 00000000..17296503
--- /dev/null
+++ b/tests/modules/abacas/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: ABACAS {
+ ext.args = '-m -p nucmer'
+ }
+
+}
diff --git a/tests/modules/abacas/test.yml b/tests/modules/abacas/test.yml
index 899bc4db..c466a6ed 100644
--- a/tests/modules/abacas/test.yml
+++ b/tests/modules/abacas/test.yml
@@ -1,5 +1,5 @@
- name: abacas
- command: nextflow run ./tests/modules/abacas -entry test_abacas -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/abacas -entry test_abacas -c ./tests/config/nextflow.config -c ./tests/modules/abacas/nextflow.config
tags:
- abacas
files:
diff --git a/tests/modules/adapterremoval/main.nf b/tests/modules/adapterremoval/main.nf
index 9dd37aa9..ee7f1c44 100644
--- a/tests/modules/adapterremoval/main.nf
+++ b/tests/modules/adapterremoval/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf' addParams( options: [:] )
+include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf'
workflow test_adapterremoval_single_end {
input = [ [ id:'test', single_end:true, collapse:false ], // meta map
diff --git a/tests/modules/adapterremoval/nextflow.config b/tests/modules/adapterremoval/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/adapterremoval/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/adapterremoval/test.yml b/tests/modules/adapterremoval/test.yml
index 318e7866..a6c4a6cf 100644
--- a/tests/modules/adapterremoval/test.yml
+++ b/tests/modules/adapterremoval/test.yml
@@ -1,5 +1,5 @@
- name: adapterremoval test_adapterremoval_single_end
- command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
tags:
- adapterremoval
files:
@@ -9,7 +9,7 @@
md5sum: 62139afee94defad5b83bdd0b8475a1f
- name: adapterremoval test_adapterremoval_paired_end
- command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
tags:
- adapterremoval
files:
@@ -21,7 +21,7 @@
md5sum: de7b38e2c881bced8671acb1ab452d78
- name: adapterremoval test_adapterremoval_paired_end_collapse
- command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
tags:
- adapterremoval
files:
diff --git a/tests/modules/agrvate/main.nf b/tests/modules/agrvate/main.nf
index 58058fe3..ac682bef 100644
--- a/tests/modules/agrvate/main.nf
+++ b/tests/modules/agrvate/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { AGRVATE } from '../../../modules/agrvate/main.nf' addParams( options: ["args": "--mummer"] )
+include { AGRVATE } from '../../../modules/agrvate/main.nf'
workflow test_agrvate {
diff --git a/tests/modules/agrvate/nextflow.config b/tests/modules/agrvate/nextflow.config
new file mode 100644
index 00000000..7f127e5e
--- /dev/null
+++ b/tests/modules/agrvate/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: AGRVATE {
+ ext.args = '--mummer'
+ }
+
+}
diff --git a/tests/modules/agrvate/test.yml b/tests/modules/agrvate/test.yml
index ec413663..36e8886c 100644
--- a/tests/modules/agrvate/test.yml
+++ b/tests/modules/agrvate/test.yml
@@ -1,5 +1,5 @@
- name: agrvate
- command: nextflow run ./tests/modules/agrvate -entry test_agrvate -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/agrvate -entry test_agrvate -c ./tests/config/nextflow.config -c ./tests/modules/agrvate/nextflow.config
tags:
- agrvate
files:
diff --git a/tests/modules/allelecounter/main.nf b/tests/modules/allelecounter/main.nf
index b938ab94..3fe11be3 100644
--- a/tests/modules/allelecounter/main.nf
+++ b/tests/modules/allelecounter/main.nf
@@ -1,7 +1,7 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
-include { ALLELECOUNTER } from '../../../modules/allelecounter/main.nf' addParams( options: [:] )
+include { ALLELECOUNTER } from '../../../modules/allelecounter/main.nf'
workflow test_allelecounter_bam {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/allelecounter/nextflow.config b/tests/modules/allelecounter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/allelecounter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/allelecounter/test.yml b/tests/modules/allelecounter/test.yml
index bbef0ecc..a0afbc12 100644
--- a/tests/modules/allelecounter/test.yml
+++ b/tests/modules/allelecounter/test.yml
@@ -1,5 +1,5 @@
- name: allelecounter test_allelecounter_bam
- command: nextflow run tests/modules/allelecounter -entry test_allelecounter_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/allelecounter -entry test_allelecounter_bam -c ./tests/config/nextflow.config -c ./tests/modules/allelecounter/nextflow.config
tags:
- allelecounter
files:
@@ -7,7 +7,7 @@
md5sum: 2bbe9d7331b78bdac30fe30dbc5fdaf3
- name: allelecounter test_allelecounter_cram
- command: nextflow run tests/modules/allelecounter -entry test_allelecounter_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/allelecounter -entry test_allelecounter_cram -c ./tests/config/nextflow.config -c ./tests/modules/allelecounter/nextflow.config
tags:
- allelecounter
files:
diff --git a/tests/modules/amps/main.nf b/tests/modules/amps/main.nf
index 7d7a40d1..15572096 100644
--- a/tests/modules/amps/main.nf
+++ b/tests/modules/amps/main.nf
@@ -2,12 +2,12 @@
nextflow.enable.dsl = 2
-include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf' addParams( options: [:] )
-include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf' addParams( options: [:] )
-include { MALT_BUILD } from '../../../modules/malt/build/main.nf' addParams( options: [:] )
-include { MALT_RUN } from '../../../modules/malt/run/main.nf' addParams( options: [:] )
-include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' addParams( options: [args: "-f def_anc"] )
-include { AMPS } from '../../../modules/amps/main.nf' addParams( options: [:] )
+include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf'
+include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf'
+include { MALT_BUILD } from '../../../modules/malt/build/main.nf'
+include { MALT_RUN } from '../../../modules/malt/run/main.nf'
+include { MALTEXTRACT } from '../../../modules/maltextract/main.nf'
+include { AMPS } from '../../../modules/amps/main.nf'
workflow test_amps {
diff --git a/tests/modules/amps/nextflow.config b/tests/modules/amps/nextflow.config
new file mode 100644
index 00000000..b58ac3fe
--- /dev/null
+++ b/tests/modules/amps/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: MALTEXTRACT {
+ ext.args = '-f def_anc'
+ }
+
+}
diff --git a/tests/modules/amps/test.yml b/tests/modules/amps/test.yml
index 04691f18..f38320e4 100644
--- a/tests/modules/amps/test.yml
+++ b/tests/modules/amps/test.yml
@@ -1,5 +1,5 @@
- name: amps
- command: nextflow run ./tests/modules/amps -entry test_amps -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/amps -entry test_amps -c ./tests/config/nextflow.config -c ./tests/modules/amps/nextflow.config
tags:
- amps
files:
diff --git a/tests/modules/arriba/main.nf b/tests/modules/arriba/main.nf
index 833742d6..60741275 100644
--- a/tests/modules/arriba/main.nf
+++ b/tests/modules/arriba/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { STAR_GENOMEGENERATE } from '../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 11'] )
-include { STAR_ALIGN } from '../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'] )
-include { ARRIBA } from '../../../modules/arriba/main.nf' addParams( options: [:] )
+include { STAR_GENOMEGENERATE } from '../../../modules/star/genomegenerate/main.nf'
+include { STAR_ALIGN } from '../../../modules/star/align/main.nf'
+include { ARRIBA } from '../../../modules/arriba/main.nf'
workflow test_arriba_single_end {
@@ -14,9 +14,12 @@ workflow test_arriba_single_end {
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+ star_ignore_sjdbgtf = false
+ seq_platform = 'illumina'
+ seq_center = false
STAR_GENOMEGENERATE ( fasta, gtf )
- STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
+ STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
}
@@ -29,8 +32,11 @@ workflow test_arriba_paired_end {
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+ star_ignore_sjdbgtf = false
+ seq_platform = 'illumina'
+ seq_center = false
STAR_GENOMEGENERATE ( fasta, gtf )
- STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
+ STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
}
diff --git a/tests/modules/arriba/nextflow.config b/tests/modules/arriba/nextflow.config
new file mode 100644
index 00000000..1b66d8df
--- /dev/null
+++ b/tests/modules/arriba/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: STAR_GENOMEGENERATE {
+ ext.args = '--genomeSAindexNbases 11'
+ }
+
+ withName: STAR_ALIGN {
+ ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'
+ }
+
+}
diff --git a/tests/modules/arriba/test.yml b/tests/modules/arriba/test.yml
index c1dc7c1e..52743167 100644
--- a/tests/modules/arriba/test.yml
+++ b/tests/modules/arriba/test.yml
@@ -1,5 +1,5 @@
- name: arriba test_arriba_single_end
- command: nextflow run tests/modules/arriba -entry test_arriba_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/arriba/nextflow.config
tags:
- arriba
files:
@@ -7,46 +7,45 @@
md5sum: cad8c215b938d1e45b747a5b7898a4c2
- path: output/arriba/test.fusions.tsv
md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
- - path: output/index/star/Genome
+ - path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/star/Log.out
- - path: output/index/star/SA
+ - path: output/star/star/Log.out
+ - path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/star/SAindex
+ - path: output/star/star/SAindex
md5sum: 9f085c626553b1c52f2827421972ac10
- - path: output/index/star/chrLength.txt
+ - path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/star/chrName.txt
+ - path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/star/chrNameLength.txt
+ - path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/star/chrStart.txt
+ - path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/star/exonGeTrInfo.tab
+ - path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/star/exonInfo.tab
+ - path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/star/geneInfo.tab
+ - path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/star/genomeParameters.txt
+ - path: output/star/star/genomeParameters.txt
md5sum: 9e42067b1ec70b773257529230dd7b3a
- - path: output/index/star/sjdbInfo.txt
+ - path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/star/sjdbList.fromGTF.out.tab
+ - path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/star/sjdbList.out.tab
+ - path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/star/transcriptInfo.tab
+ - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
- md5sum: 29c99195dcc79ff4df1f754ff16aac78
- path: output/star/test.Log.final.out
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
- path: output/star/test.SJ.out.tab
- name: arriba test_arriba_paired_end
- command: nextflow run tests/modules/arriba -entry test_arriba_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/arriba/nextflow.config
tags:
- arriba
files:
@@ -54,39 +53,38 @@
md5sum: 85e36c887464e4deaa65f45174d3b8fd
- path: output/arriba/test.fusions.tsv
md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
- - path: output/index/star/Genome
+ - path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/star/Log.out
- - path: output/index/star/SA
+ - path: output/star/star/Log.out
+ - path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/star/SAindex
+ - path: output/star/star/SAindex
md5sum: 9f085c626553b1c52f2827421972ac10
- - path: output/index/star/chrLength.txt
+ - path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/star/chrName.txt
+ - path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/star/chrNameLength.txt
+ - path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/star/chrStart.txt
+ - path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/star/exonGeTrInfo.tab
+ - path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/star/exonInfo.tab
+ - path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/star/geneInfo.tab
+ - path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/star/genomeParameters.txt
+ - path: output/star/star/genomeParameters.txt
md5sum: 9e42067b1ec70b773257529230dd7b3a
- - path: output/index/star/sjdbInfo.txt
+ - path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/star/sjdbList.fromGTF.out.tab
+ - path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/star/sjdbList.out.tab
+ - path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/star/transcriptInfo.tab
+ - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
- md5sum: d724ca90a102347b9c5052a33ea4d308
- path: output/star/test.Log.final.out
- path: output/star/test.Log.out
- path: output/star/test.Log.progress.out
diff --git a/tests/modules/artic/guppyplex/main.nf b/tests/modules/artic/guppyplex/main.nf
index 972a6e66..89f67c74 100644
--- a/tests/modules/artic/guppyplex/main.nf
+++ b/tests/modules/artic/guppyplex/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ARTIC_GUPPYPLEX } from '../../../../modules/artic/guppyplex/main.nf' addParams( options: [:] )
+include { ARTIC_GUPPYPLEX } from '../../../../modules/artic/guppyplex/main.nf'
process STAGE_FASTQ_DIR {
input:
diff --git a/tests/modules/artic/guppyplex/nextflow.config b/tests/modules/artic/guppyplex/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/artic/guppyplex/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/artic/guppyplex/test.yml b/tests/modules/artic/guppyplex/test.yml
index 133f0b15..6fd10898 100644
--- a/tests/modules/artic/guppyplex/test.yml
+++ b/tests/modules/artic/guppyplex/test.yml
@@ -1,5 +1,5 @@
- name: artic guppyplex
- command: nextflow run tests/modules/artic/guppyplex -entry test_artic_guppyplex -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/artic/guppyplex -entry test_artic_guppyplex -c ./tests/config/nextflow.config -c ./tests/modules/artic/guppyplex/nextflow.config
tags:
- artic
- artic/guppyplex
diff --git a/tests/modules/artic/minion/main.nf b/tests/modules/artic/minion/main.nf
index f4993289..ca66ede0 100644
--- a/tests/modules/artic/minion/main.nf
+++ b/tests/modules/artic/minion/main.nf
@@ -3,17 +3,19 @@
nextflow.enable.dsl = 2
include { UNTAR } from '../../../../modules/untar/main.nf'
-include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf' addParams( fast5_dir: true, sequencing_summary: true, artic_minion_medaka_model:false )
+include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf'
workflow test_artic_minion {
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
- fast5_tar = [ file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
- sequencing_summary = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
- fasta = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true) ]
- bed = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true) ]
- dummy_file = [ ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+ ]
+ fast5_tar = file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true)
+ sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
+ fasta = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
+ bed = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
+ dummy_file = []
fast5_dir = UNTAR ( fast5_tar ).untar
diff --git a/tests/modules/artic/minion/nextflow.config b/tests/modules/artic/minion/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/artic/minion/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/artic/minion/test.yml b/tests/modules/artic/minion/test.yml
index b3c5f0f1..8b36b224 100644
--- a/tests/modules/artic/minion/test.yml
+++ b/tests/modules/artic/minion/test.yml
@@ -1,5 +1,5 @@
- name: artic minion
- command: nextflow run tests/modules/artic/minion -entry test_artic_minion -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/artic/minion -entry test_artic_minion -c ./tests/config/nextflow.config -c ./tests/modules/artic/minion/nextflow.config
tags:
- artic
- artic/minion
diff --git a/tests/modules/assemblyscan/main.nf b/tests/modules/assemblyscan/main.nf
index 6f3cbb5e..7cd5f393 100644
--- a/tests/modules/assemblyscan/main.nf
+++ b/tests/modules/assemblyscan/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ASSEMBLYSCAN } from '../../../modules/assemblyscan/main.nf' addParams( options: [:] )
+include { ASSEMBLYSCAN } from '../../../modules/assemblyscan/main.nf'
workflow test_assemblyscan {
diff --git a/tests/modules/assemblyscan/nextflow.config b/tests/modules/assemblyscan/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/assemblyscan/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/assemblyscan/test.yml b/tests/modules/assemblyscan/test.yml
index 0eb4ad66..4a3ba5ec 100644
--- a/tests/modules/assemblyscan/test.yml
+++ b/tests/modules/assemblyscan/test.yml
@@ -1,5 +1,5 @@
- name: assemblyscan test_assemblyscan
- command: nextflow run tests/modules/assemblyscan -entry test_assemblyscan -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/assemblyscan -entry test_assemblyscan -c ./tests/config/nextflow.config -c ./tests/modules/assemblyscan/nextflow.config
tags:
- assemblyscan
files:
diff --git a/tests/modules/ataqv/ataqv/main.nf b/tests/modules/ataqv/ataqv/main.nf
index 2f2a62eb..b1103350 100644
--- a/tests/modules/ataqv/ataqv/main.nf
+++ b/tests/modules/ataqv/ataqv/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf' addParams( options: [:] )
-include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../modules/ataqv/ataqv/main.nf' addParams( options: ['args': '--log-problematic-reads'] )
+include { ATAQV_ATAQV } from '../../../../modules/ataqv/ataqv/main.nf'
+include { ATAQV_ATAQV as ATAQV_ATAQV_PROBLEM_READS} from '../../../../modules/ataqv/ataqv/main.nf'
workflow test_ataqv_ataqv {
diff --git a/tests/modules/ataqv/ataqv/nextflow.config b/tests/modules/ataqv/ataqv/nextflow.config
new file mode 100644
index 00000000..31700510
--- /dev/null
+++ b/tests/modules/ataqv/ataqv/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: ATAQV_ATAQV_PROBLEM_READS {
+ ext.args = '--log-problematic-reads'
+ }
+
+}
diff --git a/tests/modules/ataqv/ataqv/test.yml b/tests/modules/ataqv/ataqv/test.yml
index 77452f6f..f9f2a888 100644
--- a/tests/modules/ataqv/ataqv/test.yml
+++ b/tests/modules/ataqv/ataqv/test.yml
@@ -1,5 +1,5 @@
- name: ataqv ataqv test_ataqv_ataqv
- command: nextflow run tests/modules/ataqv/ataqv -entry test_ataqv_ataqv -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
tags:
- ataqv
- ataqv/ataqv
@@ -9,7 +9,7 @@
- '"forward_mate_reads": 101'
- name: ataqv ataqv test_ataqv_ataqv_problem_reads
- command: nextflow run tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
tags:
- ataqv
- ataqv/ataqv
@@ -21,7 +21,7 @@
- '"forward_mate_reads": 101'
- name: ataqv ataqv test_ataqv_ataqv_peak
- command: nextflow run tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_peak -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_peak -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
tags:
- ataqv
- ataqv/ataqv
@@ -31,7 +31,7 @@
- '"forward_mate_reads": 101'
- name: ataqv ataqv test_ataqv_ataqv_tss
- command: nextflow run tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_tss -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_tss -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
tags:
- ataqv
- ataqv/ataqv
@@ -41,7 +41,7 @@
- '"forward_mate_reads": 101'
- name: ataqv ataqv test_ataqv_ataqv_excluded_regs
- command: nextflow run tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config
tags:
- ataqv
- ataqv/ataqv
diff --git a/tests/modules/bakta/main.nf b/tests/modules/bakta/main.nf
index 531099f1..1bc00622 100644
--- a/tests/modules/bakta/main.nf
+++ b/tests/modules/bakta/main.nf
@@ -2,12 +2,14 @@
nextflow.enable.dsl = 2
-include { BAKTA } from '../../../modules/bakta/main.nf' addParams( options: [:] )
+include { BAKTA } from '../../../modules/bakta/main.nf'
workflow test_bakta {
-
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+ ]
BAKTA ( input, [], [], [] )
}
diff --git a/tests/modules/bakta/nextflow.config b/tests/modules/bakta/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bakta/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bamaligncleaner/main.nf b/tests/modules/bamaligncleaner/main.nf
index 94ee005f..c9d517ae 100644
--- a/tests/modules/bamaligncleaner/main.nf
+++ b/tests/modules/bamaligncleaner/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BAMALIGNCLEANER } from '../../../modules/bamaligncleaner/main.nf' addParams( options: [:] )
+include { BAMALIGNCLEANER } from '../../../modules/bamaligncleaner/main.nf'
workflow test_bamaligncleaner {
diff --git a/tests/modules/bamaligncleaner/nextflow.config b/tests/modules/bamaligncleaner/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bamaligncleaner/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bamaligncleaner/test.yml b/tests/modules/bamaligncleaner/test.yml
index 568925b0..4207b8c2 100644
--- a/tests/modules/bamaligncleaner/test.yml
+++ b/tests/modules/bamaligncleaner/test.yml
@@ -1,5 +1,5 @@
- name: bamaligncleaner
- command: nextflow run ./tests/modules/bamaligncleaner -entry test_bamaligncleaner -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bamaligncleaner -entry test_bamaligncleaner -c ./tests/config/nextflow.config -c ./tests/modules/bamaligncleaner/nextflow.config
tags:
- bamaligncleaner
files:
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 5538c86f..eb0bed01 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf' addParams( options: [args:"-reference"] )
+include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
workflow test_bamtools_split {
diff --git a/tests/modules/bamtools/split/nextflow.config b/tests/modules/bamtools/split/nextflow.config
new file mode 100644
index 00000000..e7de5477
--- /dev/null
+++ b/tests/modules/bamtools/split/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BAMTOOLS_SPLIT {
+ ext.args = '-reference'
+ }
+
+}
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index f28a9bcf..4f52e9ce 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,5 +1,5 @@
- name: bamtools split test_bamtools_split
- command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
tags:
- bamtools/split
- bamtools
diff --git a/tests/modules/bamutil/trimbam/main.nf b/tests/modules/bamutil/trimbam/main.nf
index 3699756c..2967b038 100644
--- a/tests/modules/bamutil/trimbam/main.nf
+++ b/tests/modules/bamutil/trimbam/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BAMUTIL_TRIMBAM } from '../../../../modules/bamutil/trimbam/main.nf' addParams( options: [:] )
+include { BAMUTIL_TRIMBAM } from '../../../../modules/bamutil/trimbam/main.nf'
workflow test_bamutil_trimbam {
diff --git a/tests/modules/bamutil/trimbam/nextflow.config b/tests/modules/bamutil/trimbam/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bamutil/trimbam/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bamutil/trimbam/test.yml b/tests/modules/bamutil/trimbam/test.yml
index 95ddc3b3..443a4ded 100644
--- a/tests/modules/bamutil/trimbam/test.yml
+++ b/tests/modules/bamutil/trimbam/test.yml
@@ -1,5 +1,5 @@
- name: bamutil trimbam test_bamutil_trimbam
- command: nextflow run tests/modules/bamutil/trimbam -entry test_bamutil_trimbam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bamutil/trimbam -entry test_bamutil_trimbam -c ./tests/config/nextflow.config -c ./tests/modules/bamutil/trimbam/nextflow.config
tags:
- bamutil/trimbam
- bamutil
diff --git a/tests/modules/bandage/image/main.nf b/tests/modules/bandage/image/main.nf
index 524066b0..15f01ab1 100644
--- a/tests/modules/bandage/image/main.nf
+++ b/tests/modules/bandage/image/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BANDAGE_IMAGE } from '../../../../modules/bandage/image/main.nf' addParams( options: [:] )
+include { BANDAGE_IMAGE } from '../../../../modules/bandage/image/main.nf'
workflow test_bandage_image {
input = [
diff --git a/tests/modules/bandage/image/nextflow.config b/tests/modules/bandage/image/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bandage/image/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bandage/image/test.yml b/tests/modules/bandage/image/test.yml
index 437eca05..2abdd175 100644
--- a/tests/modules/bandage/image/test.yml
+++ b/tests/modules/bandage/image/test.yml
@@ -1,5 +1,5 @@
- name: bandage image
- command: nextflow run ./tests/modules/bandage/image -entry test_bandage_image -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bandage/image -entry test_bandage_image -c ./tests/config/nextflow.config -c ./tests/modules/bandage/image/nextflow.config
tags:
- bandage
- bandage/image
diff --git a/tests/modules/bbmap/align/main.nf b/tests/modules/bbmap/align/main.nf
index c3bf43ba..c7a02e2a 100644
--- a/tests/modules/bbmap/align/main.nf
+++ b/tests/modules/bbmap/align/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams( options: [:] )
-include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf' addParams( options: [:] )
-include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf' addParams( options: [args: "unpigz=t" ] )
+include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf'
+include { BBMAP_ALIGN } from '../../../../modules/bbmap/align/main.nf'
+include { BBMAP_ALIGN as BBMAP_ALIGN_PIGZ } from '../../../../modules/bbmap/align/main.nf'
workflow test_bbmap_align_paired_end_fasta_ref {
diff --git a/tests/modules/bbmap/align/nextflow.config b/tests/modules/bbmap/align/nextflow.config
new file mode 100644
index 00000000..fe0afd72
--- /dev/null
+++ b/tests/modules/bbmap/align/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BBMAP_ALIGN_PIGZ {
+ ext.args = 'unpigz=t'
+ }
+
+}
diff --git a/tests/modules/bbmap/align/test.yml b/tests/modules/bbmap/align/test.yml
index a30713c9..d9f9a862 100644
--- a/tests/modules/bbmap/align/test.yml
+++ b/tests/modules/bbmap/align/test.yml
@@ -1,5 +1,5 @@
- name: bbmap align paired end fasta ref
- command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_fasta_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
tags:
- bbmap
- bbmap/align
@@ -9,7 +9,7 @@
- path: output/bbmap/test.bbmap.log
- name: bbmap align paired end index ref
- command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
tags:
- bbmap
- bbmap/align
@@ -19,7 +19,7 @@
- path: output/bbmap/test.bbmap.log
- name: bbmap align single end index ref
- command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_single_end_index_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
tags:
- bbmap
- bbmap/align
@@ -29,7 +29,7 @@
- path: output/bbmap/test.bbmap.log
- name: bbmap align paired end index ref pigz
- command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/align -entry test_bbmap_align_paired_end_index_ref_pigz -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/align/nextflow.config
tags:
- bbmap
- bbmap/align
diff --git a/tests/modules/bbmap/bbduk/main.nf b/tests/modules/bbmap/bbduk/main.nf
index 911ca391..e1f0c2de 100644
--- a/tests/modules/bbmap/bbduk/main.nf
+++ b/tests/modules/bbmap/bbduk/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BBMAP_BBDUK } from '../../../../modules/bbmap/bbduk/main.nf' addParams( options: [ 'args' : 'trimq=10 qtrim=r', 'suffix' : '.trim' ] )
+include { BBMAP_BBDUK } from '../../../../modules/bbmap/bbduk/main.nf'
workflow test_bbmap_bbduk_single_end {
diff --git a/tests/modules/bbmap/bbduk/nextflow.config b/tests/modules/bbmap/bbduk/nextflow.config
new file mode 100644
index 00000000..8940a9be
--- /dev/null
+++ b/tests/modules/bbmap/bbduk/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BBMAP_BBDUK {
+ ext.args = 'trimq=10 qtrim=r'
+ ext.suffix = '.trim'
+ }
+
+}
diff --git a/tests/modules/bbmap/bbduk/test.yml b/tests/modules/bbmap/bbduk/test.yml
index 4d2b8604..7ab5b963 100644
--- a/tests/modules/bbmap/bbduk/test.yml
+++ b/tests/modules/bbmap/bbduk/test.yml
@@ -1,5 +1,5 @@
- name: bbmap bbduk test_bbmap_bbduk_single_end
- command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
tags:
- bbmap/bbduk
files:
@@ -10,7 +10,7 @@
md5sum: a87d0cbd5ced7df8bf1751e4cb407482
- name: bbmap bbduk test_bbmap_bbduk_paired_end
- command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
tags:
- bbmap/bbduk
files:
@@ -23,7 +23,7 @@
md5sum: 406e068fbe198f02b48e7e210cc0c69f
- name: bbmap bbduk test_bbmap_bbduk_se_ref
- command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_se_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
tags:
- bbmap/bbduk
files:
@@ -34,7 +34,7 @@
md5sum: 3970e82605c7d109bb348fc94e9eecc0
- name: bbmap bbduk test_bbmap_bbduk_pe_ref
- command: nextflow run tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/bbduk -entry test_bbmap_bbduk_pe_ref -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbduk/nextflow.config
tags:
- bbmap/bbduk
files:
diff --git a/tests/modules/bbmap/bbsplit/main.nf b/tests/modules/bbmap/bbsplit/main.nf
index 1d3c30c1..d1236061 100644
--- a/tests/modules/bbmap/bbsplit/main.nf
+++ b/tests/modules/bbmap/bbsplit/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/bbmap/bbsplit/main.nf' addParams( options: [:] )
-include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/bbmap/bbsplit/main.nf' addParams( options: [:] )
+include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_INDEX } from '../../../../modules/bbmap/bbsplit/main.nf'
+include { BBMAP_BBSPLIT as BBMAP_BBSPLIT_SPLIT } from '../../../../modules/bbmap/bbsplit/main.nf'
workflow test_bbmap_bbsplit {
diff --git a/tests/modules/bbmap/bbsplit/nextflow.config b/tests/modules/bbmap/bbsplit/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bbmap/bbsplit/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bbmap/bbsplit/test.yml b/tests/modules/bbmap/bbsplit/test.yml
index 87bdebea..add9b519 100644
--- a/tests/modules/bbmap/bbsplit/test.yml
+++ b/tests/modules/bbmap/bbsplit/test.yml
@@ -1,5 +1,5 @@
- name: bbmap bbsplit test_bbmap_bbsplit
- command: nextflow run tests/modules/bbmap/bbsplit -entry test_bbmap_bbsplit -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/bbsplit -entry test_bbmap_bbsplit -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/bbsplit/nextflow.config
tags:
- bbmap/bbsplit
- bbmap
diff --git a/tests/modules/bbmap/index/main.nf b/tests/modules/bbmap/index/main.nf
index 0d912615..a6f111f4 100644
--- a/tests/modules/bbmap/index/main.nf
+++ b/tests/modules/bbmap/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams( options: [:] )
+include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf'
workflow test_bbmap_index {
diff --git a/tests/modules/bbmap/index/nextflow.config b/tests/modules/bbmap/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bbmap/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bbmap/index/test.yml b/tests/modules/bbmap/index/test.yml
index 32684ad4..4e8d7196 100644
--- a/tests/modules/bbmap/index/test.yml
+++ b/tests/modules/bbmap/index/test.yml
@@ -1,7 +1,5 @@
-## TODO nf-core: Please run the following command to build this file:
-# nf-core modules create-test-yml bbmap/index
- name: bbmap index
- command: nextflow run ./tests/modules/bbmap/index -entry test_bbmap_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bbmap/index -entry test_bbmap_index -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/index/nextflow.config
tags:
- bbmap
- bbmap/index
diff --git a/tests/modules/bcftools/concat/main.nf b/tests/modules/bcftools/concat/main.nf
index 8869a3d7..8441d488 100644
--- a/tests/modules/bcftools/concat/main.nf
+++ b/tests/modules/bcftools/concat/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf' addParams( options: ['args': '--no-version'] )
+include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
workflow test_bcftools_concat {
diff --git a/tests/modules/bcftools/concat/nextflow.config b/tests/modules/bcftools/concat/nextflow.config
new file mode 100644
index 00000000..3f0d064a
--- /dev/null
+++ b/tests/modules/bcftools/concat/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_CONCAT {
+ ext.args = '--no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/concat/test.yml b/tests/modules/bcftools/concat/test.yml
index 413fe798..fee6158f 100644
--- a/tests/modules/bcftools/concat/test.yml
+++ b/tests/modules/bcftools/concat/test.yml
@@ -1,5 +1,5 @@
- name: bcftools concat test_bcftools_concat
- command: nextflow run tests/modules/bcftools/concat -entry test_bcftools_concat -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
tags:
- bcftools/concat
- bcftools
diff --git a/tests/modules/bcftools/consensus/main.nf b/tests/modules/bcftools/consensus/main.nf
index 13f7b39e..ab00fbce 100644
--- a/tests/modules/bcftools/consensus/main.nf
+++ b/tests/modules/bcftools/consensus/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_CONSENSUS } from '../../../../modules/bcftools/consensus/main.nf' addParams( options: [:] )
+include { BCFTOOLS_CONSENSUS } from '../../../../modules/bcftools/consensus/main.nf'
workflow test_bcftools_consensus {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/bcftools/consensus/nextflow.config b/tests/modules/bcftools/consensus/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bcftools/consensus/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bcftools/consensus/test.yml b/tests/modules/bcftools/consensus/test.yml
index b3760fcd..7fa4ecae 100644
--- a/tests/modules/bcftools/consensus/test.yml
+++ b/tests/modules/bcftools/consensus/test.yml
@@ -1,5 +1,5 @@
- name: bcftools consensus test_bcftools_consensus
- command: nextflow run tests/modules/bcftools/consensus -entry test_bcftools_consensus -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/consensus -entry test_bcftools_consensus -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/consensus/nextflow.config
tags:
- bcftools/consensus
- bcftools
diff --git a/tests/modules/bcftools/filter/main.nf b/tests/modules/bcftools/filter/main.nf
index bd419e3a..85fbf950 100644
--- a/tests/modules/bcftools/filter/main.nf
+++ b/tests/modules/bcftools/filter/main.nf
@@ -3,7 +3,7 @@
nextflow.enable.dsl = 2
//keep --no-verson argument, otherwise md5 will change on each execution
-include { BCFTOOLS_FILTER } from '../../../../modules/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
+include { BCFTOOLS_FILTER } from '../../../../modules/bcftools/filter/main.nf'
workflow test_bcftools_filter {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/bcftools/filter/nextflow.config b/tests/modules/bcftools/filter/nextflow.config
new file mode 100644
index 00000000..68cac7bb
--- /dev/null
+++ b/tests/modules/bcftools/filter/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_FILTER {
+ ext.args = '--no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/filter/test.yml b/tests/modules/bcftools/filter/test.yml
index 0f8e48eb..da842538 100644
--- a/tests/modules/bcftools/filter/test.yml
+++ b/tests/modules/bcftools/filter/test.yml
@@ -1,5 +1,5 @@
- name: bcftools filter test_bcftools_filter
- command: nextflow run tests/modules/bcftools/filter -entry test_bcftools_filter -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/filter -entry test_bcftools_filter -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/filter/nextflow.config
tags:
- bcftools/filter
- bcftools
diff --git a/tests/modules/bcftools/index/main.nf b/tests/modules/bcftools/index/main.nf
index 73909d66..839cd988 100644
--- a/tests/modules/bcftools/index/main.nf
+++ b/tests/modules/bcftools/index/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../modules/bcftools/index/main.nf' addParams( options: [:] )
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../modules/bcftools/index/main.nf' addParams( options: [args: '-t'] )
+include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_CSI } from '../../../../modules/bcftools/index/main.nf'
+include { BCFTOOLS_INDEX as BCFTOOLS_INDEX_TBI } from '../../../../modules/bcftools/index/main.nf'
workflow test_bcftools_index_csi {
diff --git a/tests/modules/bcftools/index/nextflow.config b/tests/modules/bcftools/index/nextflow.config
new file mode 100644
index 00000000..9a060ba2
--- /dev/null
+++ b/tests/modules/bcftools/index/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_INDEX_TBI {
+ ext.args = '-t'
+ }
+
+}
diff --git a/tests/modules/bcftools/index/test.yml b/tests/modules/bcftools/index/test.yml
index 36c5f3c0..f1a29437 100644
--- a/tests/modules/bcftools/index/test.yml
+++ b/tests/modules/bcftools/index/test.yml
@@ -1,5 +1,5 @@
- name: bcftools index
- command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_csi -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config
tags:
- bcftools
- bcftools/index
@@ -8,7 +8,7 @@
md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd
- name: bcftools index tbi
- command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_tbi -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/index -entry test_bcftools_index_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/index/nextflow.config
tags:
- bcftools
- bcftools/index
diff --git a/tests/modules/bcftools/isec/main.nf b/tests/modules/bcftools/isec/main.nf
index 1b0c2c07..0b8ffc5c 100644
--- a/tests/modules/bcftools/isec/main.nf
+++ b/tests/modules/bcftools/isec/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_ISEC } from '../../../../modules/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
+include { BCFTOOLS_ISEC } from '../../../../modules/bcftools/isec/main.nf'
workflow test_bcftools_isec {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/bcftools/isec/nextflow.config b/tests/modules/bcftools/isec/nextflow.config
new file mode 100644
index 00000000..770e4674
--- /dev/null
+++ b/tests/modules/bcftools/isec/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_ISEC {
+ ext.args = '--nfiles +2 --output-type z --no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/isec/test.yml b/tests/modules/bcftools/isec/test.yml
index 92186c89..fc887d9d 100644
--- a/tests/modules/bcftools/isec/test.yml
+++ b/tests/modules/bcftools/isec/test.yml
@@ -1,5 +1,5 @@
- name: bcftools isec test_bcftools_isec
- command: nextflow run tests/modules/bcftools/isec -entry test_bcftools_isec -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/isec -entry test_bcftools_isec -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/isec/nextflow.config
tags:
- bcftools
- bcftools/isec
diff --git a/tests/modules/bcftools/merge/main.nf b/tests/modules/bcftools/merge/main.nf
index a672a9a7..119e237a 100644
--- a/tests/modules/bcftools/merge/main.nf
+++ b/tests/modules/bcftools/merge/main.nf
@@ -3,7 +3,7 @@
nextflow.enable.dsl = 2
//keep --no-verson argument, otherwise md5 will change on each execution
-include { BCFTOOLS_MERGE } from '../../../../modules/bcftools/merge/main.nf' addParams( options: ['args': '--force-samples --no-version'] )
+include { BCFTOOLS_MERGE } from '../../../../modules/bcftools/merge/main.nf'
workflow test_bcftools_merge {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/bcftools/merge/nextflow.config b/tests/modules/bcftools/merge/nextflow.config
new file mode 100644
index 00000000..e11e50b6
--- /dev/null
+++ b/tests/modules/bcftools/merge/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_MERGE {
+ ext.args = '--force-samples --no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/merge/test.yml b/tests/modules/bcftools/merge/test.yml
index d3cdd74a..6c9dd556 100644
--- a/tests/modules/bcftools/merge/test.yml
+++ b/tests/modules/bcftools/merge/test.yml
@@ -1,5 +1,5 @@
- name: bcftools merge test_bcftools_merge
- command: nextflow run tests/modules/bcftools/merge -entry test_bcftools_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/merge -entry test_bcftools_merge -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/merge/nextflow.config
tags:
- bcftools/merge
- bcftools
diff --git a/tests/modules/bcftools/mpileup/main.nf b/tests/modules/bcftools/mpileup/main.nf
index 2225c5e0..813ca408 100644
--- a/tests/modules/bcftools/mpileup/main.nf
+++ b/tests/modules/bcftools/mpileup/main.nf
@@ -2,8 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf' addParams( options: ['args2': '--no-version --ploidy 1 --multiallelic-caller',
- 'args3': '--no-version' ] )
+include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
workflow test_bcftools_mpileup {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/bcftools/mpileup/nextflow.config b/tests/modules/bcftools/mpileup/nextflow.config
new file mode 100644
index 00000000..c21fef8d
--- /dev/null
+++ b/tests/modules/bcftools/mpileup/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_MPILEUP {
+ ext.args2 = '--no-version --ploidy 1 --multiallelic-caller'
+ ext.args3 = '--no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/mpileup/test.yml b/tests/modules/bcftools/mpileup/test.yml
index 71877e29..f081c543 100644
--- a/tests/modules/bcftools/mpileup/test.yml
+++ b/tests/modules/bcftools/mpileup/test.yml
@@ -1,5 +1,5 @@
- name: bcftools mpileup test_bcftools_mpileup
- command: nextflow run tests/modules/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
tags:
- bcftools/mpileup
- bcftools
diff --git a/tests/modules/bcftools/norm/main.nf b/tests/modules/bcftools/norm/main.nf
index 046c0b3c..ac056bea 100644
--- a/tests/modules/bcftools/norm/main.nf
+++ b/tests/modules/bcftools/norm/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_NORM } from '../../../../modules/bcftools/norm/main.nf' addParams( options: ['args': '-m -any --no-version'] )
+include { BCFTOOLS_NORM } from '../../../../modules/bcftools/norm/main.nf'
workflow test_bcftools_norm {
diff --git a/tests/modules/bcftools/norm/nextflow.config b/tests/modules/bcftools/norm/nextflow.config
new file mode 100644
index 00000000..e4d27a73
--- /dev/null
+++ b/tests/modules/bcftools/norm/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_NORM {
+ ext.args = '-m -any --no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/norm/test.yml b/tests/modules/bcftools/norm/test.yml
index 40d0cc7e..bb4f9aca 100644
--- a/tests/modules/bcftools/norm/test.yml
+++ b/tests/modules/bcftools/norm/test.yml
@@ -1,5 +1,5 @@
- name: bcftools norm
- command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config
tags:
- bcftools
- bcftools/norm
diff --git a/tests/modules/bcftools/query/main.nf b/tests/modules/bcftools/query/main.nf
index a16ceddf..733cae17 100644
--- a/tests/modules/bcftools/query/main.nf
+++ b/tests/modules/bcftools/query/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_QUERY } from '../../../../modules/bcftools/query/main.nf' addParams( options: ['args': "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'" ] )
+include { BCFTOOLS_QUERY } from '../../../../modules/bcftools/query/main.nf'
workflow test_bcftools_query {
diff --git a/tests/modules/bcftools/query/nextflow.config b/tests/modules/bcftools/query/nextflow.config
new file mode 100644
index 00000000..e4105006
--- /dev/null
+++ b/tests/modules/bcftools/query/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_QUERY {
+ ext.args = "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'"
+ }
+
+}
diff --git a/tests/modules/bcftools/query/test.yml b/tests/modules/bcftools/query/test.yml
index fbfda92b..aaa9af7b 100644
--- a/tests/modules/bcftools/query/test.yml
+++ b/tests/modules/bcftools/query/test.yml
@@ -1,5 +1,5 @@
- name: bcftools query
- command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/query/nextflow.config
tags:
- bcftools
- bcftools/query
@@ -8,7 +8,7 @@
md5sum: c32a6d28f185822d8fe1eeb7e42ec155
- name: bcftools query with optional files
- command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query_with_optional_files -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/query -entry test_bcftools_query_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/query/nextflow.config
tags:
- bcftools
- bcftools/query
diff --git a/tests/modules/bcftools/reheader/main.nf b/tests/modules/bcftools/reheader/main.nf
index 40863331..d1dcd8b8 100644
--- a/tests/modules/bcftools/reheader/main.nf
+++ b/tests/modules/bcftools/reheader/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf' addParams( options: [suffix: '.updated'] )
+include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf'
workflow test_bcftools_reheader_update_sequences {
diff --git a/tests/modules/bcftools/reheader/nextflow.config b/tests/modules/bcftools/reheader/nextflow.config
new file mode 100644
index 00000000..a377b26d
--- /dev/null
+++ b/tests/modules/bcftools/reheader/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_REHEADER {
+ ext.suffix = '.updated'
+ }
+
+}
diff --git a/tests/modules/bcftools/reheader/test.yml b/tests/modules/bcftools/reheader/test.yml
index 78337206..1ce0b104 100644
--- a/tests/modules/bcftools/reheader/test.yml
+++ b/tests/modules/bcftools/reheader/test.yml
@@ -1,5 +1,5 @@
- name: bcftools reheader test_bcftools_reheader_update_sequences
- command: nextflow run tests/modules/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
tags:
- bcftools/reheader
- bcftools
@@ -8,7 +8,7 @@
md5sum: 9e29f28038bfce77ee00022627209ed6
- name: bcftools reheader test_bcftools_reheader_new_header
- command: nextflow run tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
tags:
- bcftools/reheader
- bcftools
@@ -17,7 +17,7 @@
md5sum: f7f536d889bbf5be40243252c394ee1f
- name: bcftools reheader test_bcftools_reheader_new_header_update_sequences
- command: nextflow run tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/reheader -entry test_bcftools_reheader_new_header_update_sequences -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/reheader/nextflow.config
tags:
- bcftools/reheader
- bcftools
diff --git a/tests/modules/bcftools/stats/main.nf b/tests/modules/bcftools/stats/main.nf
index 4039c080..808a3330 100644
--- a/tests/modules/bcftools/stats/main.nf
+++ b/tests/modules/bcftools/stats/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_STATS } from '../../../../modules/bcftools/stats/main.nf' addParams( options: [:] )
+include { BCFTOOLS_STATS } from '../../../../modules/bcftools/stats/main.nf'
workflow test_bcftools_stats {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/bcftools/stats/nextflow.config b/tests/modules/bcftools/stats/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bcftools/stats/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bcftools/stats/test.yml b/tests/modules/bcftools/stats/test.yml
index cd25fe66..d3587f95 100644
--- a/tests/modules/bcftools/stats/test.yml
+++ b/tests/modules/bcftools/stats/test.yml
@@ -1,5 +1,5 @@
- name: bcftools stats test_bcftools_stats
- command: nextflow run tests/modules/bcftools/stats -entry test_bcftools_stats -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/stats -entry test_bcftools_stats -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/stats/nextflow.config
tags:
- bcftools
- bcftools/stats
diff --git a/tests/modules/bcftools/view/main.nf b/tests/modules/bcftools/view/main.nf
index a8ac3b31..f45d0284 100644
--- a/tests/modules/bcftools/view/main.nf
+++ b/tests/modules/bcftools/view/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BCFTOOLS_VIEW } from '../../../../modules/bcftools/view/main.nf' addParams( options: ['args': '--no-version'] )
+include { BCFTOOLS_VIEW } from '../../../../modules/bcftools/view/main.nf'
workflow test_bcftools_view {
diff --git a/tests/modules/bcftools/view/nextflow.config b/tests/modules/bcftools/view/nextflow.config
new file mode 100644
index 00000000..e1723b89
--- /dev/null
+++ b/tests/modules/bcftools/view/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BCFTOOLS_VIEW {
+ ext.args = '--no-version'
+ }
+
+}
diff --git a/tests/modules/bcftools/view/test.yml b/tests/modules/bcftools/view/test.yml
index 179e9a1c..fa926dd6 100644
--- a/tests/modules/bcftools/view/test.yml
+++ b/tests/modules/bcftools/view/test.yml
@@ -1,5 +1,5 @@
- name: bcftools view
- command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config
tags:
- bcftools
- bcftools/view
@@ -8,7 +8,7 @@
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
- name: bcftools view with optional files
- command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view_with_optional_files -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bcftools/view -entry test_bcftools_view_with_optional_files -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/view/nextflow.config
tags:
- bcftools
- bcftools/view
diff --git a/tests/modules/bedtools/bamtobed/main.nf b/tests/modules/bedtools/bamtobed/main.nf
index 41cf460a..e7635a3d 100644
--- a/tests/modules/bedtools/bamtobed/main.nf
+++ b/tests/modules/bedtools/bamtobed/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_BAMTOBED } from '../../../../modules/bedtools/bamtobed/main.nf' addParams( options: [:] )
+include { BEDTOOLS_BAMTOBED } from '../../../../modules/bedtools/bamtobed/main.nf'
workflow test_bedtools_bamtobed {
input = [ [ id:'test'], //meta map
diff --git a/tests/modules/bedtools/bamtobed/nextflow.config b/tests/modules/bedtools/bamtobed/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bedtools/bamtobed/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bedtools/bamtobed/test.yml b/tests/modules/bedtools/bamtobed/test.yml
index 106d125d..b038467c 100644
--- a/tests/modules/bedtools/bamtobed/test.yml
+++ b/tests/modules/bedtools/bamtobed/test.yml
@@ -1,5 +1,5 @@
- name: bedtools bamtobed
- command: nextflow run ./tests/modules/bedtools/bamtobed -entry test_bedtools_bamtobed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/bamtobed -entry test_bedtools_bamtobed -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/bamtobed/nextflow.config
tags:
- bedtools
- bedtools/bamtobed
diff --git a/tests/modules/bedtools/complement/main.nf b/tests/modules/bedtools/complement/main.nf
index 6456fe60..a1cca033 100644
--- a/tests/modules/bedtools/complement/main.nf
+++ b/tests/modules/bedtools/complement/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_COMPLEMENT } from '../../../../modules/bedtools/complement/main.nf' addParams( options: [suffix: '_out'] )
+include { BEDTOOLS_COMPLEMENT } from '../../../../modules/bedtools/complement/main.nf'
workflow test_bedtools_complement {
input = [ [ id:'test'],
diff --git a/tests/modules/bedtools/complement/nextflow.config b/tests/modules/bedtools/complement/nextflow.config
new file mode 100644
index 00000000..561fdead
--- /dev/null
+++ b/tests/modules/bedtools/complement/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_COMPLEMENT {
+ ext.suffix = '_out'
+ }
+
+}
diff --git a/tests/modules/bedtools/complement/test.yml b/tests/modules/bedtools/complement/test.yml
index 2ebc6419..9dbeb36f 100644
--- a/tests/modules/bedtools/complement/test.yml
+++ b/tests/modules/bedtools/complement/test.yml
@@ -1,5 +1,5 @@
- name: bedtools complement
- command: nextflow run ./tests/modules/bedtools/complement -entry test_bedtools_complement -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/complement -entry test_bedtools_complement -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/complement/nextflow.config
tags:
- bedtools
- bedtools/complement
diff --git a/tests/modules/bedtools/genomecov/main.nf b/tests/modules/bedtools/genomecov/main.nf
index 445ed078..b507a2cd 100644
--- a/tests/modules/bedtools/genomecov/main.nf
+++ b/tests/modules/bedtools/genomecov/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf' addParams( options: [suffix: '_out'] )
+include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf'
workflow test_bedtools_genomecov_noscale {
input = [
diff --git a/tests/modules/bedtools/genomecov/nextflow.config b/tests/modules/bedtools/genomecov/nextflow.config
new file mode 100644
index 00000000..bc0e4aaf
--- /dev/null
+++ b/tests/modules/bedtools/genomecov/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_GENOMECOV {
+ ext.suffix = '_out'
+ }
+
+}
diff --git a/tests/modules/bedtools/genomecov/test.yml b/tests/modules/bedtools/genomecov/test.yml
index 477e6555..8f63bde9 100644
--- a/tests/modules/bedtools/genomecov/test.yml
+++ b/tests/modules/bedtools/genomecov/test.yml
@@ -1,5 +1,5 @@
- name: bedtools genomecov test_bedtools_genomecov_noscale
- command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_noscale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
tags:
- bedtools
- bedtools/genomecov
@@ -8,7 +8,7 @@
md5sum: 66083198daca6c001d328ba9616e9b53
- name: bedtools genomecov test_bedtools_genomecov_nonbam_noscale
- command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_noscale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
tags:
- bedtools
- bedtools/genomecov
@@ -17,7 +17,7 @@
md5sum: f47b58840087426e5b643d8dfd155c1f
- name: bedtools genomecov test_bedtools_genomecov_scale
- command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_scale -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_scale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
tags:
- bedtools
- bedtools/genomecov
@@ -26,7 +26,7 @@
md5sum: 01291b6e1beab72e046653e709eb0e10
- name: bedtools genomecov test_bedtools_genomecov_nonbam_scale
- command: nextflow run tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/genomecov -entry test_bedtools_genomecov_nonbam_scale -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/genomecov/nextflow.config
tags:
- bedtools
- bedtools/genomecov
diff --git a/tests/modules/bedtools/getfasta/main.nf b/tests/modules/bedtools/getfasta/main.nf
index 194597ae..425c49d5 100644
--- a/tests/modules/bedtools/getfasta/main.nf
+++ b/tests/modules/bedtools/getfasta/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_GETFASTA } from '../../../../modules/bedtools/getfasta/main.nf' addParams( options: [:] )
+include { BEDTOOLS_GETFASTA } from '../../../../modules/bedtools/getfasta/main.nf'
workflow test_bedtools_getfasta {
bed = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
diff --git a/tests/modules/bedtools/getfasta/nextflow.config b/tests/modules/bedtools/getfasta/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bedtools/getfasta/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bedtools/getfasta/test.yml b/tests/modules/bedtools/getfasta/test.yml
index adf10da5..a455f861 100644
--- a/tests/modules/bedtools/getfasta/test.yml
+++ b/tests/modules/bedtools/getfasta/test.yml
@@ -1,5 +1,5 @@
- name: bedtools getfasta
- command: nextflow run ./tests/modules/bedtools/getfasta -entry test_bedtools_getfasta -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/getfasta -entry test_bedtools_getfasta -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/getfasta/nextflow.config
tags:
- bedtools
- bedtools/getfasta
diff --git a/tests/modules/bedtools/intersect/main.nf b/tests/modules/bedtools/intersect/main.nf
index 73a9b30c..c17d03e6 100644
--- a/tests/modules/bedtools/intersect/main.nf
+++ b/tests/modules/bedtools/intersect/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_INTERSECT } from '../../../../modules/bedtools/intersect/main.nf' addParams( options: [suffix: '_out'] )
+include { BEDTOOLS_INTERSECT } from '../../../../modules/bedtools/intersect/main.nf'
workflow test_bedtools_intersect {
input = [
diff --git a/tests/modules/bedtools/intersect/nextflow.config b/tests/modules/bedtools/intersect/nextflow.config
new file mode 100644
index 00000000..c7d0c826
--- /dev/null
+++ b/tests/modules/bedtools/intersect/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_INTERSECT {
+ ext.suffix = '_out'
+ }
+
+}
diff --git a/tests/modules/bedtools/intersect/test.yml b/tests/modules/bedtools/intersect/test.yml
index c8c3ad6e..86fe70cd 100644
--- a/tests/modules/bedtools/intersect/test.yml
+++ b/tests/modules/bedtools/intersect/test.yml
@@ -1,5 +1,5 @@
- name: bedtools intersect test_bedtools_intersect
- command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/intersect/nextflow.config
tags:
- bedtools
- bedtools/intersect
@@ -8,7 +8,7 @@
md5sum: afcbf01c2f2013aad71dbe8e34f2c15c
- name: bedtools intersect test_bedtools_intersect_bam
- command: nextflow run tests/modules/bedtools/intersect -entry test_bedtools_intersect_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/intersect -entry test_bedtools_intersect_bam -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/intersect/nextflow.config
tags:
- bedtools
- bedtools/intersect
diff --git a/tests/modules/bedtools/makewindows/main.nf b/tests/modules/bedtools/makewindows/main.nf
index 23c40a75..ce37de72 100644
--- a/tests/modules/bedtools/makewindows/main.nf
+++ b/tests/modules/bedtools/makewindows/main.nf
@@ -2,13 +2,14 @@
nextflow.enable.dsl = 2
-test_options = ['args': '-w 50 ']
-include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf' addParams( options: test_options )
+include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf'
workflow test_bedtools_makewindows {
-
- input = [ [ id:'test'],
- file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+
+ input = [
+ [ id:'test'],
+ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+ ]
BEDTOOLS_MAKEWINDOWS ( input, true )
}
diff --git a/tests/modules/bedtools/makewindows/nextflow.config b/tests/modules/bedtools/makewindows/nextflow.config
new file mode 100644
index 00000000..e8b8c3ea
--- /dev/null
+++ b/tests/modules/bedtools/makewindows/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_MAKEWINDOWS {
+ ext.args = '-w 50 '
+ }
+
+}
diff --git a/tests/modules/bedtools/makewindows/test.yml b/tests/modules/bedtools/makewindows/test.yml
index c39d1c08..8accaa36 100644
--- a/tests/modules/bedtools/makewindows/test.yml
+++ b/tests/modules/bedtools/makewindows/test.yml
@@ -1,5 +1,5 @@
- name: bedtools makewindows test_bedtools_makewindows
- command: nextflow run tests/modules/bedtools/makewindows -entry test_bedtools_makewindows -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/makewindows -entry test_bedtools_makewindows -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/makewindows/nextflow.config
tags:
- bedtools/makewindows
- bedtools
diff --git a/tests/modules/bedtools/maskfasta/main.nf b/tests/modules/bedtools/maskfasta/main.nf
index 8c30fbdc..0da02ad3 100644
--- a/tests/modules/bedtools/maskfasta/main.nf
+++ b/tests/modules/bedtools/maskfasta/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_MASKFASTA } from '../../../../modules/bedtools/maskfasta/main.nf' addParams( options: [:] )
+include { BEDTOOLS_MASKFASTA } from '../../../../modules/bedtools/maskfasta/main.nf'
workflow test_bedtools_maskfasta {
bed = [ [ id:'test'],
diff --git a/tests/modules/bedtools/maskfasta/nextflow.config b/tests/modules/bedtools/maskfasta/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bedtools/maskfasta/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bedtools/maskfasta/test.yml b/tests/modules/bedtools/maskfasta/test.yml
index f536a6eb..f1e8f35a 100644
--- a/tests/modules/bedtools/maskfasta/test.yml
+++ b/tests/modules/bedtools/maskfasta/test.yml
@@ -1,5 +1,5 @@
- name: bedtools maskfasta
- command: nextflow run ./tests/modules/bedtools/maskfasta -entry test_bedtools_maskfasta -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/maskfasta -entry test_bedtools_maskfasta -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/maskfasta/nextflow.config
tags:
- bedtools
- bedtools/maskfasta
diff --git a/tests/modules/bedtools/merge/main.nf b/tests/modules/bedtools/merge/main.nf
index f11b804a..5fca0526 100644
--- a/tests/modules/bedtools/merge/main.nf
+++ b/tests/modules/bedtools/merge/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_MERGE } from '../../../../modules/bedtools/merge/main.nf' addParams( options: [suffix: '_out'] )
+include { BEDTOOLS_MERGE } from '../../../../modules/bedtools/merge/main.nf'
workflow test_bedtools_merge {
input = [ [ id:'test'],
diff --git a/tests/modules/bedtools/merge/nextflow.config b/tests/modules/bedtools/merge/nextflow.config
new file mode 100644
index 00000000..e7d635dd
--- /dev/null
+++ b/tests/modules/bedtools/merge/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_MERGE {
+ ext.suffix = '_out'
+ }
+
+}
diff --git a/tests/modules/bedtools/merge/test.yml b/tests/modules/bedtools/merge/test.yml
index 62bc6860..5fc8b034 100644
--- a/tests/modules/bedtools/merge/test.yml
+++ b/tests/modules/bedtools/merge/test.yml
@@ -1,5 +1,5 @@
- name: bedtools merge
- command: nextflow run ./tests/modules/bedtools/merge -entry test_bedtools_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/merge -entry test_bedtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/merge/nextflow.config
tags:
- bedtools
- bedtools/merge
diff --git a/tests/modules/bedtools/slop/main.nf b/tests/modules/bedtools/slop/main.nf
index 47c19781..e7136fdc 100644
--- a/tests/modules/bedtools/slop/main.nf
+++ b/tests/modules/bedtools/slop/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_SLOP } from '../../../../modules/bedtools/slop/main.nf' addParams( options: [args: '-l 15 -r 30', suffix: '_out'] )
+include { BEDTOOLS_SLOP } from '../../../../modules/bedtools/slop/main.nf'
workflow test_bedtools_slop {
input = [ [ id:'test'],
diff --git a/tests/modules/bedtools/slop/nextflow.config b/tests/modules/bedtools/slop/nextflow.config
new file mode 100644
index 00000000..5dc03727
--- /dev/null
+++ b/tests/modules/bedtools/slop/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_SLOP {
+ ext.args = '-l 15 -r 30'
+ ext.suffix = '_out'
+ }
+
+}
diff --git a/tests/modules/bedtools/slop/test.yml b/tests/modules/bedtools/slop/test.yml
index 859b569e..0d49e66b 100644
--- a/tests/modules/bedtools/slop/test.yml
+++ b/tests/modules/bedtools/slop/test.yml
@@ -1,5 +1,5 @@
- name: bedtools slop
- command: nextflow run ./tests/modules/bedtools/slop -entry test_bedtools_slop -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/slop -entry test_bedtools_slop -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/slop/nextflow.config
tags:
- bedtools
- bedtools/slop
diff --git a/tests/modules/bedtools/sort/main.nf b/tests/modules/bedtools/sort/main.nf
index b5d34e2f..342b4116 100644
--- a/tests/modules/bedtools/sort/main.nf
+++ b/tests/modules/bedtools/sort/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_SORT } from '../../../../modules/bedtools/sort/main.nf' addParams( options: [suffix: '_out'] )
+include { BEDTOOLS_SORT } from '../../../../modules/bedtools/sort/main.nf'
workflow test_bedtools_sort {
input = [ [ id:'test'],
diff --git a/tests/modules/bedtools/sort/nextflow.config b/tests/modules/bedtools/sort/nextflow.config
new file mode 100644
index 00000000..6bb73232
--- /dev/null
+++ b/tests/modules/bedtools/sort/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BEDTOOLS_SORT {
+ ext.suffix = '_out'
+ }
+
+}
diff --git a/tests/modules/bedtools/sort/test.yml b/tests/modules/bedtools/sort/test.yml
index 1dd04507..173f0587 100644
--- a/tests/modules/bedtools/sort/test.yml
+++ b/tests/modules/bedtools/sort/test.yml
@@ -1,5 +1,5 @@
- name: bedtools sort
- command: nextflow run ./tests/modules/bedtools/sort -entry test_bedtools_sort -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/sort -entry test_bedtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/sort/nextflow.config
tags:
- bedtools
- bedtools/sort
diff --git a/tests/modules/bedtools/subtract/main.nf b/tests/modules/bedtools/subtract/main.nf
index 9997f08c..2a0e6eab 100644
--- a/tests/modules/bedtools/subtract/main.nf
+++ b/tests/modules/bedtools/subtract/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BEDTOOLS_SUBTRACT } from '../../../../modules/bedtools/subtract/main.nf' addParams( options: [:] )
+include { BEDTOOLS_SUBTRACT } from '../../../../modules/bedtools/subtract/main.nf'
workflow test_bedtools_subtract {
input = [
diff --git a/tests/modules/bedtools/subtract/nextflow.config b/tests/modules/bedtools/subtract/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bedtools/subtract/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bedtools/subtract/test.yml b/tests/modules/bedtools/subtract/test.yml
index fd8660fc..52b57436 100644
--- a/tests/modules/bedtools/subtract/test.yml
+++ b/tests/modules/bedtools/subtract/test.yml
@@ -1,5 +1,5 @@
- name: bedtools subtract
- command: nextflow run ./tests/modules/bedtools/subtract -entry test_bedtools_subtract -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bedtools/subtract -entry test_bedtools_subtract -c ./tests/config/nextflow.config -c ./tests/modules/bedtools/subtract/nextflow.config
tags:
- bedtools
- bedtools/subtract
diff --git a/tests/modules/bismark/align/main.nf b/tests/modules/bismark/align/main.nf
index 1f1fcdce..fe6d616a 100644
--- a/tests/modules/bismark/align/main.nf
+++ b/tests/modules/bismark/align/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' addParams( options: [:] )
-include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../modules/bismark/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
-include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../modules/bismark/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
+include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf'
+include { BISMARK_ALIGN as BISMARK_ALIGN_SE } from '../../../../modules/bismark/align/main.nf'
+include { BISMARK_ALIGN as BISMARK_ALIGN_PE } from '../../../../modules/bismark/align/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/bismark/align/nextflow.config b/tests/modules/bismark/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bismark/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bismark/align/test.yml b/tests/modules/bismark/align/test.yml
index 42dc44b3..ffae05af 100644
--- a/tests/modules/bismark/align/test.yml
+++ b/tests/modules/bismark/align/test.yml
@@ -1,19 +1,19 @@
- name: bismark align single-end test workflow
- command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bismark/align/nextflow.config
tags:
- bismark
- bismark/align
files:
- - path: output/test_single_end/test.methylated_1_bismark_bt2.bam
+ - path: output/bismark/test.methylated_1_bismark_bt2.bam
md5sum: dca4ba9ff705b70446f812e59bdb1a32
- - path: output/test_single_end/test.methylated_1_bismark_bt2_SE_report.txt
+ - path: output/bismark/test.methylated_1_bismark_bt2_SE_report.txt
- name: bismark align paired-end test workflow
- command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/align -entry test_bismark_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bismark/align/nextflow.config
tags:
- bismark
- bismark/align
files:
- - path: output/test_paired_end/test.methylated_1_bismark_bt2_pe.bam
+ - path: output/bismark/test.methylated_1_bismark_bt2_pe.bam
md5sum: 43943b1f30d056fcbd9ed26061ea0583
- - path: output/test_paired_end/test.methylated_1_bismark_bt2_PE_report.txt
+ - path: output/bismark/test.methylated_1_bismark_bt2_PE_report.txt
diff --git a/tests/modules/bismark/deduplicate/main.nf b/tests/modules/bismark/deduplicate/main.nf
index fc44745c..ad97d66a 100644
--- a/tests/modules/bismark/deduplicate/main.nf
+++ b/tests/modules/bismark/deduplicate/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' addParams( options: [:] )
+include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf'
workflow test_bismark_deduplicate {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/bismark/deduplicate/nextflow.config b/tests/modules/bismark/deduplicate/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bismark/deduplicate/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bismark/deduplicate/test.yml b/tests/modules/bismark/deduplicate/test.yml
index 604c1023..12099750 100644
--- a/tests/modules/bismark/deduplicate/test.yml
+++ b/tests/modules/bismark/deduplicate/test.yml
@@ -1,5 +1,5 @@
- name: bismark deduplicate test workflow
- command: nextflow run ./tests/modules/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/deduplicate -entry test_bismark_deduplicate -c ./tests/config/nextflow.config -c ./tests/modules/bismark/deduplicate/nextflow.config
tags:
- bismark
- bismark/deduplicate
diff --git a/tests/modules/bismark/genomepreparation/main.nf b/tests/modules/bismark/genomepreparation/main.nf
index ab847171..a9111af3 100644
--- a/tests/modules/bismark/genomepreparation/main.nf
+++ b/tests/modules/bismark/genomepreparation/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf'
workflow test_bismark_genomepreparation {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/bismark/genomepreparation/nextflow.config b/tests/modules/bismark/genomepreparation/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bismark/genomepreparation/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bismark/genomepreparation/test.yml b/tests/modules/bismark/genomepreparation/test.yml
index 15a7e7d6..a0d3c072 100644
--- a/tests/modules/bismark/genomepreparation/test.yml
+++ b/tests/modules/bismark/genomepreparation/test.yml
@@ -1,5 +1,5 @@
- name: bismark genomepreparation test workflow
- command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/genomepreparation -entry test_bismark_genomepreparation -c ./tests/config/nextflow.config -c ./tests/modules/bismark/genomepreparation/nextflow.config
tags:
- bismark
- bismark/genomepreparation
diff --git a/tests/modules/bismark/methylationextractor/main.nf b/tests/modules/bismark/methylationextractor/main.nf
index 0b3f77a1..ed857fe8 100644
--- a/tests/modules/bismark/methylationextractor/main.nf
+++ b/tests/modules/bismark/methylationextractor/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' addParams( options: [:] )
-include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf'
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf'
workflow test_bismark_methylationextractor {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/bismark/methylationextractor/nextflow.config b/tests/modules/bismark/methylationextractor/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bismark/methylationextractor/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bismark/methylationextractor/test.yml b/tests/modules/bismark/methylationextractor/test.yml
index 4505c428..f25b7646 100644
--- a/tests/modules/bismark/methylationextractor/test.yml
+++ b/tests/modules/bismark/methylationextractor/test.yml
@@ -1,5 +1,5 @@
- name: bismark methylation extractor test workflow
- command: nextflow run ./tests/modules/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/methylationextractor -entry test_bismark_methylationextractor -c ./tests/config/nextflow.config -c ./tests/modules/bismark/methylationextractor/nextflow.config
tags:
- bismark
- bismark/methylationextractor
diff --git a/tests/modules/bismark/report/main.nf b/tests/modules/bismark/report/main.nf
index 945d24ed..f80fb2bc 100644
--- a/tests/modules/bismark/report/main.nf
+++ b/tests/modules/bismark/report/main.nf
@@ -2,11 +2,11 @@
nextflow.enable.dsl = 2
-include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' addParams( options: [:] )
-include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf' addParams( options: [:] )
-include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' addParams( options: [:] )
-include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' addParams( options: [:] )
-include { BISMARK_REPORT } from '../../../../modules/bismark/report/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf'
+include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf'
+include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf'
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf'
+include { BISMARK_REPORT } from '../../../../modules/bismark/report/main.nf'
workflow test_bismark_report {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/bismark/report/nextflow.config b/tests/modules/bismark/report/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bismark/report/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bismark/report/test.yml b/tests/modules/bismark/report/test.yml
index 7e85e4dd..9195994c 100644
--- a/tests/modules/bismark/report/test.yml
+++ b/tests/modules/bismark/report/test.yml
@@ -1,5 +1,5 @@
- name: bismark report test workflow
- command: nextflow run ./tests/modules/bismark/report -entry test_bismark_report -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/report -entry test_bismark_report -c ./tests/config/nextflow.config -c ./tests/modules/bismark/report/nextflow.config
tags:
- bismark
- bismark/report
diff --git a/tests/modules/bismark/summary/main.nf b/tests/modules/bismark/summary/main.nf
index 4170d19a..8eabe51f 100644
--- a/tests/modules/bismark/summary/main.nf
+++ b/tests/modules/bismark/summary/main.nf
@@ -2,11 +2,11 @@
nextflow.enable.dsl = 2
-include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf' addParams( options: [:] )
-include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf' addParams( options: [:] )
-include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf' addParams( options: [:] )
-include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf' addParams( options: [:] )
-include { BISMARK_SUMMARY } from '../../../../modules/bismark/summary/main.nf' addParams( options: [:] )
+include { BISMARK_GENOMEPREPARATION } from '../../../../modules/bismark/genomepreparation/main.nf'
+include { BISMARK_ALIGN } from '../../../../modules/bismark/align/main.nf'
+include { BISMARK_DEDUPLICATE } from '../../../../modules/bismark/deduplicate/main.nf'
+include { BISMARK_METHYLATIONEXTRACTOR } from '../../../../modules/bismark/methylationextractor/main.nf'
+include { BISMARK_SUMMARY } from '../../../../modules/bismark/summary/main.nf'
workflow test_bismark_summary {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/bismark/summary/nextflow.config b/tests/modules/bismark/summary/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bismark/summary/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bismark/summary/test.yml b/tests/modules/bismark/summary/test.yml
index 06478873..3b5196b9 100644
--- a/tests/modules/bismark/summary/test.yml
+++ b/tests/modules/bismark/summary/test.yml
@@ -1,5 +1,5 @@
- name: bismark summary test workflow
- command: nextflow run ./tests/modules/bismark/summary -entry test_bismark_summary -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bismark/summary -entry test_bismark_summary -c ./tests/config/nextflow.config -c ./tests/modules/bismark/summary/nextflow.config
tags:
- bismark
- bismark/summary
diff --git a/tests/modules/blast/blastn/main.nf b/tests/modules/blast/blastn/main.nf
index fd690dcc..3c8496dc 100644
--- a/tests/modules/blast/blastn/main.nf
+++ b/tests/modules/blast/blastn/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
-include { BLAST_BLASTN } from '../../../../modules/blast/blastn/main.nf' addParams( options: [:] )
+include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf'
+include { BLAST_BLASTN } from '../../../../modules/blast/blastn/main.nf'
workflow test_blast_blastn {
input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
diff --git a/tests/modules/blast/blastn/nextflow.config b/tests/modules/blast/blastn/nextflow.config
new file mode 100644
index 00000000..1d5a2c01
--- /dev/null
+++ b/tests/modules/blast/blastn/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BLAST_MAKEBLASTDB {
+ ext.args = '-dbtype nucl'
+ }
+
+}
diff --git a/tests/modules/blast/blastn/test.yml b/tests/modules/blast/blastn/test.yml
index 98f76921..17522c9b 100644
--- a/tests/modules/blast/blastn/test.yml
+++ b/tests/modules/blast/blastn/test.yml
@@ -1,5 +1,5 @@
- name: blast_blastn
- command: nextflow run ./tests/modules/blast/blastn -entry test_blast_blastn -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/blast/blastn -entry test_blast_blastn -c ./tests/config/nextflow.config -c ./tests/modules/blast/blastn/nextflow.config
tags:
- blast
- blast/blastn
diff --git a/tests/modules/blast/makeblastdb/main.nf b/tests/modules/blast/makeblastdb/main.nf
index 48b39f22..9d778457 100644
--- a/tests/modules/blast/makeblastdb/main.nf
+++ b/tests/modules/blast/makeblastdb/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf' addParams( options: ['args': '-dbtype nucl'] )
+include { BLAST_MAKEBLASTDB } from '../../../../modules/blast/makeblastdb/main.nf'
workflow test_blast_makeblastdb {
input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
diff --git a/tests/modules/blast/makeblastdb/nextflow.config b/tests/modules/blast/makeblastdb/nextflow.config
new file mode 100644
index 00000000..1d5a2c01
--- /dev/null
+++ b/tests/modules/blast/makeblastdb/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: BLAST_MAKEBLASTDB {
+ ext.args = '-dbtype nucl'
+ }
+
+}
diff --git a/tests/modules/blast/makeblastdb/test.yml b/tests/modules/blast/makeblastdb/test.yml
index 7df17968..3b59f3f6 100644
--- a/tests/modules/blast/makeblastdb/test.yml
+++ b/tests/modules/blast/makeblastdb/test.yml
@@ -1,5 +1,5 @@
- name: blast_makeblastdb
- command: nextflow run ./tests/modules/blast/makeblastdb -entry test_blast_makeblastdb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/blast/makeblastdb -entry test_blast_makeblastdb -c ./tests/config/nextflow.config -c ./tests/modules/blast/makeblastdb/nextflow.config
tags:
- blast
- blast/makeblastdb
diff --git a/tests/modules/bowtie/align/main.nf b/tests/modules/bowtie/align/main.nf
index b2c8059a..e773cd38 100644
--- a/tests/modules/bowtie/align/main.nf
+++ b/tests/modules/bowtie/align/main.nf
@@ -2,13 +2,16 @@
nextflow.enable.dsl = 2
-include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' addParams( options: [:] )
-include { BOWTIE_ALIGN } from '../../../../modules/bowtie/align/main.nf' addParams( options: [:] )
+include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf'
+include { BOWTIE_ALIGN } from '../../../../modules/bowtie/align/main.nf'
workflow test_bowtie_align_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE_BUILD ( fasta )
@@ -16,10 +19,13 @@ workflow test_bowtie_align_single_end {
}
workflow test_bowtie_align_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE_BUILD ( fasta )
diff --git a/tests/modules/bowtie/align/nextflow.config b/tests/modules/bowtie/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bowtie/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bowtie/align/test.yml b/tests/modules/bowtie/align/test.yml
index 76d63d68..1f8d1294 100644
--- a/tests/modules/bowtie/align/test.yml
+++ b/tests/modules/bowtie/align/test.yml
@@ -1,5 +1,5 @@
- name: bowtie align single-end
- command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/align/nextflow.config
tags:
- bowtie
- bowtie/align
@@ -7,36 +7,36 @@
- path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out
md5sum: 4b9140ceadb8a18ae9330885370f8a0b
- - path: ./output/index/bowtie/genome.3.ebwt
+ - path: ./output/bowtie/bowtie/genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: ./output/index/bowtie/genome.2.ebwt
+ - path: ./output/bowtie/bowtie/genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- - path: ./output/index/bowtie/genome.rev.2.ebwt
+ - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- - path: ./output/index/bowtie/genome.4.ebwt
+ - path: ./output/bowtie/bowtie/genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626
- - path: ./output/index/bowtie/genome.rev.1.ebwt
+ - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06
- - path: ./output/index/bowtie/genome.1.ebwt
+ - path: ./output/bowtie/bowtie/genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199
- name: bowtie align paired-end
- command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie/align -entry test_bowtie_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/align/nextflow.config
tags:
- bowtie
- bowtie/align
files:
- path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out
- - path: ./output/index/bowtie/genome.3.ebwt
+ - path: ./output/bowtie/bowtie/genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: ./output/index/bowtie/genome.2.ebwt
+ - path: ./output/bowtie/bowtie/genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- - path: ./output/index/bowtie/genome.rev.2.ebwt
+ - path: ./output/bowtie/bowtie/genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- - path: ./output/index/bowtie/genome.4.ebwt
+ - path: ./output/bowtie/bowtie/genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626
- - path: ./output/index/bowtie/genome.rev.1.ebwt
+ - path: ./output/bowtie/bowtie/genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06
- - path: ./output/index/bowtie/genome.1.ebwt
+ - path: ./output/bowtie/bowtie/genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199
diff --git a/tests/modules/bowtie/build_test/main.nf b/tests/modules/bowtie/build_test/main.nf
index a89091a8..7a36fb55 100644
--- a/tests/modules/bowtie/build_test/main.nf
+++ b/tests/modules/bowtie/build_test/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf' addParams( options: [publish_dir:'bowtie'] )
+include { BOWTIE_BUILD } from '../../../../modules/bowtie/build/main.nf'
workflow test_bowtie_build {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/bowtie/build_test/nextflow.config b/tests/modules/bowtie/build_test/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bowtie/build_test/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bowtie/build_test/test.yml b/tests/modules/bowtie/build_test/test.yml
index c6b765c9..c51d1e8a 100644
--- a/tests/modules/bowtie/build_test/test.yml
+++ b/tests/modules/bowtie/build_test/test.yml
@@ -1,5 +1,5 @@
- name: bowtie build
- command: nextflow run ./tests/modules/bowtie/build_test -entry test_bowtie_build -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie/build_test -entry test_bowtie_build -c ./tests/config/nextflow.config -c ./tests/modules/bowtie/build/nextflow.config
tags:
- bowtie
- bowtie/build
diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf
index 20602f30..8c8e3ab8 100644
--- a/tests/modules/bowtie2/align/main.nf
+++ b/tests/modules/bowtie2/align/main.nf
@@ -2,13 +2,16 @@
nextflow.enable.dsl = 2
-include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [:] )
-include { BOWTIE2_ALIGN } from '../../../../modules/bowtie2/align/main.nf' addParams( options: [:] )
+include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf'
+include { BOWTIE2_ALIGN } from '../../../../modules/bowtie2/align/main.nf'
workflow test_bowtie2_align_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE2_BUILD ( fasta )
@@ -16,11 +19,15 @@ workflow test_bowtie2_align_single_end {
}
workflow test_bowtie2_align_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}
diff --git a/tests/modules/bowtie2/align/nextflow.config b/tests/modules/bowtie2/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bowtie2/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml
index 05952b76..95d48b88 100644
--- a/tests/modules/bowtie2/align/test.yml
+++ b/tests/modules/bowtie2/align/test.yml
@@ -1,41 +1,41 @@
- name: bowtie2 align single-end
- command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- - path: ./output/index/bowtie2/genome.3.bt2
+ - path: ./output/bowtie2/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: ./output/index/bowtie2/genome.2.bt2
+ - path: ./output/bowtie2/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf
- - path: ./output/index/bowtie2/genome.1.bt2
+ - path: ./output/bowtie2/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- - path: ./output/index/bowtie2/genome.4.bt2
+ - path: ./output/bowtie2/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626
- - path: ./output/index/bowtie2/genome.rev.1.bt2
+ - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184
- - path: ./output/index/bowtie2/genome.rev.2.bt2
+ - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597
- name: bowtie2 align paired-end
- command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- - path: ./output/index/bowtie2/genome.3.bt2
+ - path: ./output/bowtie2/bowtie2/genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: ./output/index/bowtie2/genome.2.bt2
+ - path: ./output/bowtie2/bowtie2/genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf
- - path: ./output/index/bowtie2/genome.1.bt2
+ - path: ./output/bowtie2/bowtie2/genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- - path: ./output/index/bowtie2/genome.4.bt2
+ - path: ./output/bowtie2/bowtie2/genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626
- - path: ./output/index/bowtie2/genome.rev.1.bt2
+ - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184
- - path: ./output/index/bowtie2/genome.rev.2.bt2
+ - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597
diff --git a/tests/modules/bowtie2/build_test/main.nf b/tests/modules/bowtie2/build_test/main.nf
index 2b41fab2..f1d35083 100644
--- a/tests/modules/bowtie2/build_test/main.nf
+++ b/tests/modules/bowtie2/build_test/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf' addParams( options: [publish_dir:'bowtie2'] )
+include { BOWTIE2_BUILD } from '../../../../modules/bowtie2/build/main.nf'
workflow test_bowtie2_build {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/bowtie2/build_test/nextflow.config b/tests/modules/bowtie2/build_test/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bowtie2/build_test/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bowtie2/build_test/test.yml b/tests/modules/bowtie2/build_test/test.yml
index 3fd049b9..88e6c3ad 100644
--- a/tests/modules/bowtie2/build_test/test.yml
+++ b/tests/modules/bowtie2/build_test/test.yml
@@ -1,5 +1,5 @@
- name: bowtie2 build
- command: nextflow run ./tests/modules/bowtie2/build_test -entry test_bowtie2_build -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bowtie2/build_test -entry test_bowtie2_build -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/build/nextflow.config
tags:
- bowtie2
- bowtie2/build
diff --git a/tests/modules/bwa/aln/main.nf b/tests/modules/bwa/aln/main.nf
index feb7473d..909e7a2d 100644
--- a/tests/modules/bwa/aln/main.nf
+++ b/tests/modules/bwa/aln/main.nf
@@ -2,16 +2,19 @@
nextflow.enable.dsl = 2
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
-include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
+include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf'
//
// Test with single-end data
//
workflow test_bwa_aln_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
@@ -22,10 +25,13 @@ workflow test_bwa_aln_single_end {
// Test with paired-end data
//
workflow test_bwa_aln_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
diff --git a/tests/modules/bwa/aln/nextflow.config b/tests/modules/bwa/aln/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwa/aln/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwa/aln/test.yml b/tests/modules/bwa/aln/test.yml
index 08848143..c89c47be 100644
--- a/tests/modules/bwa/aln/test.yml
+++ b/tests/modules/bwa/aln/test.yml
@@ -1,24 +1,24 @@
- name: bwa aln single-end
- command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/aln/nextflow.config
tags:
- bwa
- bwa/aln
files:
- path: ./output/bwa/test.sai
md5sum: aaaf39b6814c96ca1a5eacc662adf926
- - path: ./output/index/bwa/genome.bwt
+ - path: ./output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- - path: ./output/index/bwa/genome.amb
+ - path: ./output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- - path: ./output/index/bwa/genome.ann
+ - path: ./output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- - path: ./output/index/bwa/genome.pac
+ - path: ./output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- - path: ./output/index/bwa/genome.sa
+ - path: ./output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- name: bwa aln paired-end
- command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/aln -entry test_bwa_aln_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/aln/nextflow.config
tags:
- bwa
- bwa/aln
@@ -27,13 +27,13 @@
md5sum: aaaf39b6814c96ca1a5eacc662adf926
- path: ./output/bwa/test.2.sai
md5sum: b4f185d9b4cb256dd5c377070a536124
- - path: ./output/index/bwa/genome.bwt
+ - path: ./output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- - path: ./output/index/bwa/genome.amb
+ - path: ./output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- - path: ./output/index/bwa/genome.ann
+ - path: ./output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- - path: ./output/index/bwa/genome.pac
+ - path: ./output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- - path: ./output/index/bwa/genome.sa
+ - path: ./output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/bwa/index/main.nf b/tests/modules/bwa/index/main.nf
index 30d31202..fe040cb2 100644
--- a/tests/modules/bwa/index/main.nf
+++ b/tests/modules/bwa/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [publish_dir:'bwa'] )
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
workflow test_bwa_index {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/bwa/index/nextflow.config b/tests/modules/bwa/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwa/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwa/index/test.yml b/tests/modules/bwa/index/test.yml
index 3fe8663d..a9dab91d 100644
--- a/tests/modules/bwa/index/test.yml
+++ b/tests/modules/bwa/index/test.yml
@@ -1,5 +1,5 @@
- name: bwa index test_bwa_index
- command: nextflow run tests/modules/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/index -entry test_bwa_index -c ./tests/config/nextflow.config -c ./tests/modules/bwa/index/nextflow.config
tags:
- bwa
- bwa/index
diff --git a/tests/modules/bwa/mem/main.nf b/tests/modules/bwa/mem/main.nf
index bac51d23..117cbb4d 100644
--- a/tests/modules/bwa/mem/main.nf
+++ b/tests/modules/bwa/mem/main.nf
@@ -2,16 +2,19 @@
nextflow.enable.dsl = 2
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
-include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf' addParams( options: [:] )
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
+include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf'
//
// Test with single-end data
//
workflow test_bwa_mem_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
@@ -22,10 +25,13 @@ workflow test_bwa_mem_single_end {
// Test with paired-end data
//
workflow test_bwa_mem_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
diff --git a/tests/modules/bwa/mem/nextflow.config b/tests/modules/bwa/mem/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwa/mem/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwa/mem/test.yml b/tests/modules/bwa/mem/test.yml
index df1988b5..93535043 100644
--- a/tests/modules/bwa/mem/test.yml
+++ b/tests/modules/bwa/mem/test.yml
@@ -1,35 +1,35 @@
- name: bwa mem single-end
- command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
tags:
- bwa
- bwa/mem
files:
- path: ./output/bwa/test.bam
- - path: ./output/index/bwa/genome.bwt
+ - path: ./output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- - path: ./output/index/bwa/genome.amb
+ - path: ./output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- - path: ./output/index/bwa/genome.ann
+ - path: ./output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- - path: ./output/index/bwa/genome.pac
+ - path: ./output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- - path: ./output/index/bwa/genome.sa
+ - path: ./output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- name: bwa mem paired-end
- command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/mem -entry test_bwa_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwa/mem/nextflow.config
tags:
- bwa
- bwa/mem
files:
- path: ./output/bwa/test.bam
- - path: ./output/index/bwa/genome.bwt
+ - path: ./output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- - path: ./output/index/bwa/genome.amb
+ - path: ./output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- - path: ./output/index/bwa/genome.ann
+ - path: ./output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- - path: ./output/index/bwa/genome.pac
+ - path: ./output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- - path: ./output/index/bwa/genome.sa
+ - path: ./output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
diff --git a/tests/modules/bwa/sampe/main.nf b/tests/modules/bwa/sampe/main.nf
index 017f27e5..abd25566 100644
--- a/tests/modules/bwa/sampe/main.nf
+++ b/tests/modules/bwa/sampe/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
-include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
-include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf' addParams( options: [:] )
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
+include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf'
+include { BWA_SAMPE } from '../../../../modules/bwa/sampe/main.nf'
workflow test_bwa_sampe {
diff --git a/tests/modules/bwa/sampe/nextflow.config b/tests/modules/bwa/sampe/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwa/sampe/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwa/sampe/test.yml b/tests/modules/bwa/sampe/test.yml
index ba5e704d..fb6d7708 100644
--- a/tests/modules/bwa/sampe/test.yml
+++ b/tests/modules/bwa/sampe/test.yml
@@ -1,5 +1,5 @@
- name: bwa sampe
- command: nextflow run ./tests/modules/bwa/sampe -entry test_bwa_sampe -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/sampe -entry test_bwa_sampe -c ./tests/config/nextflow.config -c ./tests/modules/bwa/sampe/nextflow.config
tags:
- bwa
- bwa/sampe
diff --git a/tests/modules/bwa/samse/main.nf b/tests/modules/bwa/samse/main.nf
index 87a7c7b1..17912c36 100644
--- a/tests/modules/bwa/samse/main.nf
+++ b/tests/modules/bwa/samse/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
-include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf' addParams( options: [:] )
-include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf' addParams( options: [:] )
+include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
+include { BWA_ALN } from '../../../../modules/bwa/aln/main.nf'
+include { BWA_SAMSE } from '../../../../modules/bwa/samse/main.nf'
workflow test_bwa_samse {
diff --git a/tests/modules/bwa/samse/nextflow.config b/tests/modules/bwa/samse/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwa/samse/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwa/samse/test.yml b/tests/modules/bwa/samse/test.yml
index 597844d4..5a2fe1e3 100644
--- a/tests/modules/bwa/samse/test.yml
+++ b/tests/modules/bwa/samse/test.yml
@@ -1,5 +1,5 @@
- name: bwa samse
- command: nextflow run ./tests/modules/bwa/samse -entry test_bwa_samse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwa/samse -entry test_bwa_samse -c ./tests/config/nextflow.config -c ./tests/modules/bwa/samse/nextflow.config
tags:
- bwa
- bwa/samse
diff --git a/tests/modules/bwamem2/index/main.nf b/tests/modules/bwamem2/index/main.nf
index bb7d0803..fe88f8f7 100644
--- a/tests/modules/bwamem2/index/main.nf
+++ b/tests/modules/bwamem2/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [publish_dir:'bwamem2'] )
+include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
workflow test_bwamem2_index {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/bwamem2/index/nextflow.config b/tests/modules/bwamem2/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwamem2/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwamem2/index/test.yml b/tests/modules/bwamem2/index/test.yml
index d9d15c53..efada6ec 100644
--- a/tests/modules/bwamem2/index/test.yml
+++ b/tests/modules/bwamem2/index/test.yml
@@ -1,5 +1,5 @@
- name: bwamem2 index
- command: nextflow run ./tests/modules/bwamem2/index -entry test_bwamem2_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwamem2/index -entry test_bwamem2_index -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/index/nextflow.config
tags:
- bwamem2
- bwamem2/index
diff --git a/tests/modules/bwamem2/mem/main.nf b/tests/modules/bwamem2/mem/main.nf
index 5abda8bb..2ab557e6 100644
--- a/tests/modules/bwamem2/mem/main.nf
+++ b/tests/modules/bwamem2/mem/main.nf
@@ -2,16 +2,19 @@
nextflow.enable.dsl = 2
-include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [:] )
-include { BWAMEM2_MEM } from '../../../../modules/bwamem2/mem/main.nf' addParams( options: [:] )
+include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf'
+include { BWAMEM2_MEM } from '../../../../modules/bwamem2/mem/main.nf'
//
// Test with single-end data
//
workflow test_bwamem2_mem_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMEM2_INDEX ( fasta )
@@ -22,10 +25,13 @@ workflow test_bwamem2_mem_single_end {
// Test with paired-end data
//
workflow test_bwamem2_mem_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMEM2_INDEX ( fasta )
diff --git a/tests/modules/bwamem2/mem/nextflow.config b/tests/modules/bwamem2/mem/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwamem2/mem/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwamem2/mem/test.yml b/tests/modules/bwamem2/mem/test.yml
index cc2fe2a8..c1724bc0 100644
--- a/tests/modules/bwamem2/mem/test.yml
+++ b/tests/modules/bwamem2/mem/test.yml
@@ -1,35 +1,35 @@
- name: bwamem2 mem single-end
- command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
tags:
- bwamem2
- bwamem2/mem
files:
- path: ./output/bwamem2/test.bam
- - path: ./output/index/bwamem2/genome.fasta.amb
+ - path: ./output/bwamem2/bwamem2/genome.fasta.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- - path: ./output/index/bwamem2/genome.fasta.pac
+ - path: ./output/bwamem2/bwamem2/genome.fasta.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- - path: ./output/index/bwamem2/genome.fasta.0123
+ - path: ./output/bwamem2/bwamem2/genome.fasta.0123
md5sum: b02870de80106104abcb03cd9463e7d8
- - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
+ - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
md5sum: d097a1b82dee375d41a1ea69895a9216
- - path: ./output/index/bwamem2/genome.fasta.ann
+ - path: ./output/bwamem2/bwamem2/genome.fasta.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- name: bwamem2 mem paired-end
- command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwamem2/mem -entry test_bwamem2_mem_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwamem2/mem/nextflow.config
tags:
- bwamem2
- bwamem2/mem
files:
- path: ./output/bwamem2/test.bam
- - path: ./output/index/bwamem2/genome.fasta.amb
+ - path: ./output/bwamem2/bwamem2/genome.fasta.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- - path: ./output/index/bwamem2/genome.fasta.pac
+ - path: ./output/bwamem2/bwamem2/genome.fasta.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- - path: ./output/index/bwamem2/genome.fasta.0123
+ - path: ./output/bwamem2/bwamem2/genome.fasta.0123
md5sum: b02870de80106104abcb03cd9463e7d8
- - path: ./output/index/bwamem2/genome.fasta.bwt.2bit.64
+ - path: ./output/bwamem2/bwamem2/genome.fasta.bwt.2bit.64
md5sum: d097a1b82dee375d41a1ea69895a9216
- - path: ./output/index/bwamem2/genome.fasta.ann
+ - path: ./output/bwamem2/bwamem2/genome.fasta.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
diff --git a/tests/modules/bwameth/align/main.nf b/tests/modules/bwameth/align/main.nf
index fb8cad6a..8066941c 100644
--- a/tests/modules/bwameth/align/main.nf
+++ b/tests/modules/bwameth/align/main.nf
@@ -2,16 +2,19 @@
nextflow.enable.dsl = 2
-include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:] )
-include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf' addParams( options: [:] )
+include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf'
+include { BWAMETH_ALIGN } from '../../../../modules/bwameth/align/main.nf'
//
// Test with single-end data
//
workflow test_bwameth_align_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMETH_INDEX ( fasta )
@@ -22,10 +25,13 @@ workflow test_bwameth_align_single_end {
// Test with paired-end data
//
workflow test_bwameth_align_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWAMETH_INDEX ( fasta )
diff --git a/tests/modules/bwameth/align/nextflow.config b/tests/modules/bwameth/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwameth/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwameth/align/test.yml b/tests/modules/bwameth/align/test.yml
index 5cf4b84d..f921b5f4 100644
--- a/tests/modules/bwameth/align/test.yml
+++ b/tests/modules/bwameth/align/test.yml
@@ -1,5 +1,5 @@
- name: bwameth align single-end test workflow
- command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/align/nextflow.config
tags:
- bwameth
- bwameth/align
@@ -7,7 +7,7 @@
- path: output/bwameth/test.bam
- name: bwameth align paired-end test workflow
- command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwameth/align -entry test_bwameth_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/align/nextflow.config
tags:
- bwameth
- bwameth/align
diff --git a/tests/modules/bwameth/index/main.nf b/tests/modules/bwameth/index/main.nf
index 46662201..b70fd1f7 100644
--- a/tests/modules/bwameth/index/main.nf
+++ b/tests/modules/bwameth/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf' addParams( options: [publish_dir:'bwameth'] )
+include { BWAMETH_INDEX } from '../../../../modules/bwameth/index/main.nf'
workflow test_bwameth_index {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/bwameth/index/nextflow.config b/tests/modules/bwameth/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/bwameth/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/bwameth/index/test.yml b/tests/modules/bwameth/index/test.yml
index 0cc7922e..9783c511 100644
--- a/tests/modules/bwameth/index/test.yml
+++ b/tests/modules/bwameth/index/test.yml
@@ -1,5 +1,5 @@
- name: bwameth index test workflow
- command: nextflow run ./tests/modules/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/bwameth/index -entry test_bwameth_index -c ./tests/config/nextflow.config -c ./tests/modules/bwameth/index/nextflow.config
tags:
- bwameth
- bwameth/index
diff --git a/tests/modules/cat/cat/main.nf b/tests/modules/cat/cat/main.nf
index a110a8ab..430c71fa 100644
--- a/tests/modules/cat/cat/main.nf
+++ b/tests/modules/cat/cat/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CAT_CAT } from '../../../../modules/cat/cat/main.nf' addParams( options: [:] )
+include { CAT_CAT } from '../../../../modules/cat/cat/main.nf'
workflow test_cat_unzipped_unzipped {
diff --git a/tests/modules/cat/cat/nextflow.config b/tests/modules/cat/cat/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cat/cat/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cat/cat/test.yml b/tests/modules/cat/cat/test.yml
index 2f234a01..d7973042 100644
--- a/tests/modules/cat/cat/test.yml
+++ b/tests/modules/cat/cat/test.yml
@@ -1,5 +1,5 @@
- name: cat unzipped unzipped
- command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
- cat
- cat/cat
@@ -8,7 +8,7 @@
md5sum: f44b33a0e441ad58b2d3700270e2dbe2
- name: cat zipped zipped
- command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
- cat
- cat/cat
@@ -16,7 +16,7 @@
- path: output/cat/cat.txt.gz
- name: cat zipped unzipped
- command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
- cat
- cat/cat
@@ -25,7 +25,7 @@
md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
- name: cat unzipped zipped
- command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
- cat
- cat/cat
diff --git a/tests/modules/cat/fastq/main.nf b/tests/modules/cat/fastq/main.nf
index 027bd108..c3da91d2 100644
--- a/tests/modules/cat/fastq/main.nf
+++ b/tests/modules/cat/fastq/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf' addParams( options: [publish_dir:'cat'] )
+include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf'
workflow test_cat_fastq_single_end {
input = [
diff --git a/tests/modules/cat/fastq/nextflow.config b/tests/modules/cat/fastq/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cat/fastq/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cat/fastq/test.yml b/tests/modules/cat/fastq/test.yml
index 9a5af25c..89ddf331 100644
--- a/tests/modules/cat/fastq/test.yml
+++ b/tests/modules/cat/fastq/test.yml
@@ -1,5 +1,5 @@
- name: cat fastq single-end
- command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
tags:
- cat
- cat/fastq
@@ -8,7 +8,7 @@
md5sum: 59f6dbe193741bb40f498f254aeb2e99
- name: cat fastq fastqc_paired_end
- command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config
tags:
- cat
- cat/fastq
diff --git a/tests/modules/cellranger/mkref/main.nf b/tests/modules/cellranger/mkref/main.nf
index b20a68db..ad98ed1a 100644
--- a/tests/modules/cellranger/mkref/main.nf
+++ b/tests/modules/cellranger/mkref/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf' addParams( options: [:] )
+include { CELLRANGER_MKREF } from '../../../../modules/cellranger/mkref/main.nf'
workflow test_cellranger_mkref {
diff --git a/tests/modules/cellranger/mkref/nextflow.config b/tests/modules/cellranger/mkref/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cellranger/mkref/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml
index 5e60819e..eb01e9e2 100644
--- a/tests/modules/cellranger/mkref/test.yml
+++ b/tests/modules/cellranger/mkref/test.yml
@@ -1,5 +1,5 @@
- name: cellranger mkref test_cellranger_mkref
- command: nextflow run tests/modules/cellranger/mkref -entry test_cellranger_mkref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
tags:
- cellranger
- cellranger/mkref
diff --git a/tests/modules/checkm/lineagewf/main.nf b/tests/modules/checkm/lineagewf/main.nf
index 94309896..e914774c 100644
--- a/tests/modules/checkm/lineagewf/main.nf
+++ b/tests/modules/checkm/lineagewf/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf' addParams( options: [:] )
+include { CHECKM_LINEAGEWF } from '../../../../modules/checkm/lineagewf/main.nf'
workflow test_checkm_lineagewf {
diff --git a/tests/modules/checkm/lineagewf/nextflow.config b/tests/modules/checkm/lineagewf/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/checkm/lineagewf/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/checkm/lineagewf/test.yml b/tests/modules/checkm/lineagewf/test.yml
index 768601b0..6749f6aa 100644
--- a/tests/modules/checkm/lineagewf/test.yml
+++ b/tests/modules/checkm/lineagewf/test.yml
@@ -1,5 +1,5 @@
- name: checkm lineagewf
- command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c ./tests/config/nextflow.config -c ./tests/modules/checkm/lineagewf/nextflow.config
tags:
- checkm
- checkm/lineagewf
@@ -16,7 +16,7 @@
- "UID1"
- name: checkm lineagewf_multi
- command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c ./tests/config/nextflow.config -c ./tests/modules/checkm/lineagewf/nextflow.config
tags:
- checkm
- checkm/lineagewf
diff --git a/tests/modules/chromap/chromap/main.nf b/tests/modules/chromap/chromap/main.nf
index a5a1fc86..5522f2b5 100644
--- a/tests/modules/chromap/chromap/main.nf
+++ b/tests/modules/chromap/chromap/main.nf
@@ -2,19 +2,20 @@
nextflow.enable.dsl = 2
-include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf' addParams( options: [:] )
-include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/chromap/chromap/main.nf' addParams( options: [:] )
-include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../modules/chromap/chromap/main.nf' addParams( options: ['args': '--SAM'] )
+include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf'
+include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_BASE } from '../../../../modules/chromap/chromap/main.nf'
+include { CHROMAP_CHROMAP as CHROMAP_CHROMAP_SAM } from '../../../../modules/chromap/chromap/main.nf'
workflow test_chromap_chromap_single_end {
// Test single-end and gz compressed output
-
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
input = [
[ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
]
+ fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
CHROMAP_INDEX ( fasta )
CHROMAP_CHROMAP_BASE (
@@ -31,8 +32,6 @@ workflow test_chromap_chromap_single_end {
workflow test_chromap_chromap_paired_end {
// Test paired-end and gz compressed output
-
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
input = [
[ id:'test', single_end:false ], // meta map
[
@@ -40,6 +39,7 @@ workflow test_chromap_chromap_paired_end {
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
+ fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
CHROMAP_INDEX ( fasta )
CHROMAP_CHROMAP_BASE (
@@ -56,8 +56,6 @@ workflow test_chromap_chromap_paired_end {
workflow test_chromap_chromap_paired_bam {
// Test paired-end and bam output
-
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
input = [
[ id:'test', single_end:false ], // meta map
[
@@ -65,6 +63,7 @@ workflow test_chromap_chromap_paired_bam {
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
]
+ fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
CHROMAP_INDEX ( fasta )
CHROMAP_CHROMAP_SAM (
diff --git a/tests/modules/chromap/chromap/nextflow.config b/tests/modules/chromap/chromap/nextflow.config
new file mode 100644
index 00000000..1e979bb9
--- /dev/null
+++ b/tests/modules/chromap/chromap/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: CHROMAP_CHROMAP_SAM {
+ ext.args = '--SAM'
+ }
+
+}
diff --git a/tests/modules/chromap/chromap/test.yml b/tests/modules/chromap/chromap/test.yml
index b2ce8137..20a51e2b 100644
--- a/tests/modules/chromap/chromap/test.yml
+++ b/tests/modules/chromap/chromap/test.yml
@@ -1,5 +1,5 @@
- name: chromap chromap test_chromap_chromap_single_end
- command: nextflow run tests/modules/chromap/chromap -entry test_chromap_chromap_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_single_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
tags:
- chromap/chromap
- chromap
@@ -10,7 +10,7 @@
md5sum: 7029066c27ac6f5ef18d660d5741979a
- name: chromap chromap test_chromap_chromap_paired_end
- command: nextflow run tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
tags:
- chromap/chromap
- chromap
@@ -21,7 +21,7 @@
md5sum: cafd8fb21977f5ae69e9008b220ab169
- name: chromap chromap test_chromap_chromap_paired_bam
- command: nextflow run tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
tags:
- chromap/chromap
- chromap
diff --git a/tests/modules/chromap/index/main.nf b/tests/modules/chromap/index/main.nf
index 997baba1..18b42006 100644
--- a/tests/modules/chromap/index/main.nf
+++ b/tests/modules/chromap/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf' addParams( options: [:] )
+include { CHROMAP_INDEX } from '../../../../modules/chromap/index/main.nf'
workflow test_chromap_index {
diff --git a/tests/modules/chromap/index/nextflow.config b/tests/modules/chromap/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/chromap/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml
index 0a99a3a0..74cfadfc 100644
--- a/tests/modules/chromap/index/test.yml
+++ b/tests/modules/chromap/index/test.yml
@@ -1,5 +1,5 @@
- name: chromap index test_chromap_index
- command: nextflow run tests/modules/chromap/index -entry test_chromap_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/chromap/index -entry test_chromap_index -c ./tests/config/nextflow.config -c ./tests/modules/chromap/index/nextflow.config
tags:
- chromap/index
- chromap
diff --git a/tests/modules/clonalframeml/main.nf b/tests/modules/clonalframeml/main.nf
index 35ecaa79..73773113 100644
--- a/tests/modules/clonalframeml/main.nf
+++ b/tests/modules/clonalframeml/main.nf
@@ -2,13 +2,15 @@
nextflow.enable.dsl = 2
-include { CLONALFRAMEML } from '../../../modules/clonalframeml/main.nf' addParams( options: [:] )
+include { CLONALFRAMEML } from '../../../modules/clonalframeml/main.nf'
workflow test_clonalframeml {
-
- input = [ [ id:'test' ], // meta map
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/species/haemophilus_influenzae/genome/genome_msa.newick", checkIfExists: true),
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/species/haemophilus_influenzae/genome/genome_msa.fa.gz", checkIfExists: true),]
+
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['haemophilus_influenzae']['genome']['genome_aln_nwk'], checkIfExists: true),
+ file(params.test_data['haemophilus_influenzae']['genome']['genome_aln_gz'], checkIfExists: true)
+ ]
CLONALFRAMEML ( input )
}
diff --git a/tests/modules/clonalframeml/nextflow.config b/tests/modules/clonalframeml/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/clonalframeml/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/clonalframeml/test.yml b/tests/modules/clonalframeml/test.yml
index f2b68115..8ea11d16 100644
--- a/tests/modules/clonalframeml/test.yml
+++ b/tests/modules/clonalframeml/test.yml
@@ -1,5 +1,5 @@
- name: clonalframeml test_clonalframeml
- command: nextflow run tests/modules/clonalframeml -entry test_clonalframeml -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/clonalframeml -entry test_clonalframeml -c ./tests/config/nextflow.config -c ./tests/modules/clonalframeml/nextflow.config
tags:
- clonalframeml
files:
diff --git a/tests/modules/cmseq/polymut/main.nf b/tests/modules/cmseq/polymut/main.nf
index 729ed38f..df6a0ac1 100644
--- a/tests/modules/cmseq/polymut/main.nf
+++ b/tests/modules/cmseq/polymut/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CMSEQ_POLYMUT } from '../../../../modules/cmseq/polymut/main.nf' addParams( options: [:] )
+include { CMSEQ_POLYMUT } from '../../../../modules/cmseq/polymut/main.nf'
workflow test_cmseq_polymut_1 {
diff --git a/tests/modules/cmseq/polymut/nextflow.config b/tests/modules/cmseq/polymut/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cmseq/polymut/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cmseq/polymut/test.yml b/tests/modules/cmseq/polymut/test.yml
index 2a989cb9..05887fa8 100644
--- a/tests/modules/cmseq/polymut/test.yml
+++ b/tests/modules/cmseq/polymut/test.yml
@@ -1,5 +1,5 @@
- name: cmseq polymut test_cmseq_polymut_1
- command: nextflow run tests/modules/cmseq/polymut -entry test_cmseq_polymut_1 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_1 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config
tags:
- cmseq/polymut
- cmseq
@@ -8,7 +8,7 @@
md5sum: fd325c1724ee23d132a9115c64494efc
- name: cmseq polymut test_cmseq_polymut_2
- command: nextflow run tests/modules/cmseq/polymut -entry test_cmseq_polymut_2 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_2 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config
tags:
- cmseq/polymut
- cmseq
@@ -17,7 +17,7 @@
md5sum: fd325c1724ee23d132a9115c64494efc
- name: cmseq polymut test_cmseq_polymut_3
- command: nextflow run tests/modules/cmseq/polymut -entry test_cmseq_polymut_3 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cmseq/polymut -entry test_cmseq_polymut_3 -c ./tests/config/nextflow.config -c ./tests/modules/cmseq/polymut/nextflow.config
tags:
- cmseq/polymut
- cmseq
diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf
index 5d92afaa..6b40dec6 100755
--- a/tests/modules/cnvkit/batch/main.nf
+++ b/tests/modules/cnvkit/batch/main.nf
@@ -2,61 +2,54 @@
nextflow.enable.dsl = 2
-include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
-include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn --method wgs' ] )
-include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--method wgs' ] )
-
+include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
workflow test_cnvkit_hybrid {
- tumor = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
- normal = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
- input = [ [ id:'test' ], // meta map
- tumor,
- normal
- ]
- fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
+ ]
+ fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+ targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
CNVKIT_HYBRID ( input, fasta, targets, [] )
}
workflow test_cnvkit_wgs {
- tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
- normal = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
- input = [ [ id:'test'], // meta map
- tumor,
- normal
- ]
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+ input = [
+ [ id:'test'], // meta map
+ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+ ]
+ fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
CNVKIT_WGS ( input, fasta, [], [] )
}
-
workflow test_cnvkit_cram {
- tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
- normal = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
- input = [ [ id:'test'], // meta map
- tumor,
- normal
- ]
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+ input = [
+ [ id:'test'], // meta map
+ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+ ]
+ fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
CNVKIT_WGS ( input, fasta, [], [] )
}
-
-
workflow test_cnvkit_tumoronly {
- tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
- input = [ [ id:'test'], // meta map
- tumor,
- [ ]
- ]
+ input = [
+ [ id:'test'], // meta map
+ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+ []
+ ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
diff --git a/tests/modules/cnvkit/batch/nextflow.config b/tests/modules/cnvkit/batch/nextflow.config
new file mode 100644
index 00000000..b8a8fc3f
--- /dev/null
+++ b/tests/modules/cnvkit/batch/nextflow.config
@@ -0,0 +1,17 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: CNVKIT_HYBRID {
+ ext.args = '--output-reference reference.cnn'
+ }
+
+ withName: CNVKIT_WGS {
+ ext.args = '--output-reference reference.cnn --method wgs'
+ }
+
+ withName: CNVKIT_TUMORONLY {
+ ext.args = '--method wgs'
+ }
+
+}
diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml
index 96ea670c..57af3603 100755
--- a/tests/modules/cnvkit/batch/test.yml
+++ b/tests/modules/cnvkit/batch/test.yml
@@ -1,5 +1,5 @@
- name: cnvkit batch test_cnvkit_hybrid
- command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit/batch
- cnvkit
@@ -28,7 +28,7 @@
md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
- name: cnvkit batch test_cnvkit_wgs
- command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit/batch
- cnvkit
@@ -59,7 +59,7 @@
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
- name: cnvkit batch test_cnvkit_cram
- command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit/batch
- cnvkit
@@ -90,7 +90,7 @@
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
- name: cnvkit batch test_cnvkit_tumoronly
- command: nextflow run tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
tags:
- cnvkit/batch
- cnvkit
diff --git a/tests/modules/cooler/cload/main.nf b/tests/modules/cooler/cload/main.nf
index dd9b3e98..170b7e11 100644
--- a/tests/modules/cooler/cload/main.nf
+++ b/tests/modules/cooler/cload/main.nf
@@ -2,12 +2,12 @@
nextflow.enable.dsl = 2
-include { COOLER_CLOAD } from '../../../../modules/cooler/cload/main.nf' addParams( options: [args:'pairix'] )
-include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/cooler/cload/main.nf' addParams( options: [args:'pairs --chrom1 1 --pos1 2 --chrom2 4 --pos2 5 -N'] )
-include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/cooler/cload/main.nf' addParams( options: [args:'tabix'] )
-include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
-include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
-include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
+include { COOLER_CLOAD } from '../../../../modules/cooler/cload/main.nf'
+include { COOLER_CLOAD as COOLER_CLOAD_PAIRS } from '../../../../modules/cooler/cload/main.nf'
+include { COOLER_CLOAD as COOLER_CLOAD_TABIX } from '../../../../modules/cooler/cload/main.nf'
+include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf'
+include { COOLER_DUMP as COOLER_DUMP_PAIRS} from '../../../../modules/cooler/dump/main.nf'
+include { COOLER_DUMP as COOLER_DUMP_TABIX} from '../../../../modules/cooler/dump/main.nf'
workflow test_cooler_cload_pairix {
diff --git a/tests/modules/cooler/cload/nextflow.config b/tests/modules/cooler/cload/nextflow.config
new file mode 100644
index 00000000..610a5425
--- /dev/null
+++ b/tests/modules/cooler/cload/nextflow.config
@@ -0,0 +1,17 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: COOLER_CLOAD {
+ ext.args = 'pairix'
+ }
+
+ withName: COOLER_CLOAD_PAIRS {
+ ext.args = 'pairs --chrom1 1 --pos1 2 --chrom2 4 --pos2 5 -N'
+ }
+
+ withName: COOLER_CLOAD_TABIX {
+ ext.args = 'tabix'
+ }
+
+}
diff --git a/tests/modules/cooler/cload/test.yml b/tests/modules/cooler/cload/test.yml
index 7cb9a0bd..f99f4624 100644
--- a/tests/modules/cooler/cload/test.yml
+++ b/tests/modules/cooler/cload/test.yml
@@ -1,5 +1,5 @@
- name: cooler cload test_cooler_cload_pairix
- command: nextflow run tests/modules/cooler/cload -entry test_cooler_cload_pairix -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_pairix -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config
tags:
- cooler/cload
- cooler
@@ -9,7 +9,7 @@
md5sum: 0cd85311089669688ec17468eae02111
- name: cooler cload test_cooler_cload_pairs
- command: nextflow run tests/modules/cooler/cload -entry test_cooler_cload_pairs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_pairs -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config
tags:
- cooler/cload
- cooler
@@ -19,7 +19,7 @@
md5sum: 7f832733fc7853ebb1937b33e4c1e0de
- name: cooler cload test_cooler_cload_tabix
- command: nextflow run tests/modules/cooler/cload -entry test_cooler_cload_tabix -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/cload -entry test_cooler_cload_tabix -c ./tests/config/nextflow.config -c ./tests/modules/cooler/cload/nextflow.config
tags:
- cooler/cload
- cooler
diff --git a/tests/modules/cooler/digest/main.nf b/tests/modules/cooler/digest/main.nf
index 817c9081..4dfa25be 100644
--- a/tests/modules/cooler/digest/main.nf
+++ b/tests/modules/cooler/digest/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { COOLER_DIGEST } from '../../../../modules/cooler/digest/main.nf' addParams( options: [:] )
+include { COOLER_DIGEST } from '../../../../modules/cooler/digest/main.nf'
workflow test_cooler_digest {
diff --git a/tests/modules/cooler/digest/nextflow.config b/tests/modules/cooler/digest/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cooler/digest/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cooler/digest/test.yml b/tests/modules/cooler/digest/test.yml
index b594a232..80430ed7 100644
--- a/tests/modules/cooler/digest/test.yml
+++ b/tests/modules/cooler/digest/test.yml
@@ -1,5 +1,5 @@
- name: cooler digest test_cooler_digest
- command: nextflow run tests/modules/cooler/digest -entry test_cooler_digest -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/digest -entry test_cooler_digest -c ./tests/config/nextflow.config -c ./tests/modules/cooler/digest/nextflow.config
tags:
- cooler/digest
- cooler
diff --git a/tests/modules/cooler/dump/main.nf b/tests/modules/cooler/dump/main.nf
index deeeb21f..d80ee0d7 100644
--- a/tests/modules/cooler/dump/main.nf
+++ b/tests/modules/cooler/dump/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
+include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf'
workflow test_cooler_dump {
diff --git a/tests/modules/cooler/dump/nextflow.config b/tests/modules/cooler/dump/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cooler/dump/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cooler/dump/test.yml b/tests/modules/cooler/dump/test.yml
index ccfc5f47..6f81c7a9 100644
--- a/tests/modules/cooler/dump/test.yml
+++ b/tests/modules/cooler/dump/test.yml
@@ -1,5 +1,5 @@
- name: cooler dump test_cooler_dump
- command: nextflow run tests/modules/cooler/dump -entry test_cooler_dump -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/dump -entry test_cooler_dump -c ./tests/config/nextflow.config -c ./tests/modules/cooler/dump/nextflow.config
tags:
- cooler/dump
- cooler
diff --git a/tests/modules/cooler/merge/main.nf b/tests/modules/cooler/merge/main.nf
index 564660c5..81336984 100644
--- a/tests/modules/cooler/merge/main.nf
+++ b/tests/modules/cooler/merge/main.nf
@@ -2,15 +2,19 @@
nextflow.enable.dsl = 2
-include { COOLER_MERGE } from '../../../../modules/cooler/merge/main.nf' addParams( options: [publish_files:[:]] )
-include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
+include { COOLER_MERGE } from '../../../../modules/cooler/merge/main.nf'
+include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf'
workflow test_cooler_merge {
- input = [ [ id:'test' ], // meta map
- [ file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true),
- file(params.test_data['generic']['cooler']['test_merge_cool_cp2'], checkIfExists: true)]
- ]
+ input = [
+ [ id:'test' ], // meta map
+ [
+ file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true),
+ file(params.test_data['generic']['cooler']['test_merge_cool_cp2'], checkIfExists: true)
+ ]
+ ]
- COOLER_MERGE ( input ).cool | COOLER_DUMP
+ COOLER_MERGE ( input )
+ COOLER_DUMP ( COOLER_MERGE.out.cool, "" )
}
diff --git a/tests/modules/cooler/merge/nextflow.config b/tests/modules/cooler/merge/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/cooler/merge/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/cooler/merge/test.yml b/tests/modules/cooler/merge/test.yml
index 3ac388e7..c884ba5e 100644
--- a/tests/modules/cooler/merge/test.yml
+++ b/tests/modules/cooler/merge/test.yml
@@ -1,5 +1,5 @@
- name: cooler merge test_cooler_merge
- command: nextflow run tests/modules/cooler/merge -entry test_cooler_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/merge -entry test_cooler_merge -c ./tests/config/nextflow.config -c ./tests/modules/cooler/merge/nextflow.config
tags:
- cooler/merge
- cooler
diff --git a/tests/modules/cooler/zoomify/main.nf b/tests/modules/cooler/zoomify/main.nf
index 72c33983..42edadb8 100644
--- a/tests/modules/cooler/zoomify/main.nf
+++ b/tests/modules/cooler/zoomify/main.nf
@@ -2,13 +2,14 @@
nextflow.enable.dsl = 2
-include { COOLER_ZOOMIFY } from '../../../../modules/cooler/zoomify/main.nf' addParams( options: ['args':'-r 2,4,8', publish_files:[:]] )
-include { COOLER_DUMP } from '../../../../modules/cooler/dump/main.nf' addParams( options: [:] )
+include { COOLER_ZOOMIFY } from '../../../../modules/cooler/zoomify/main.nf'
workflow test_cooler_zoomify {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true)]
+
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['generic']['cooler']['test_merge_cool'], checkIfExists: true)
+ ]
COOLER_ZOOMIFY ( input )
- COOLER_DUMP(COOLER_ZOOMIFY.out.mcool, "/resolutions/2")
}
diff --git a/tests/modules/cooler/zoomify/nextflow.config b/tests/modules/cooler/zoomify/nextflow.config
new file mode 100644
index 00000000..d4c3503f
--- /dev/null
+++ b/tests/modules/cooler/zoomify/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: COOLER_ZOOMIFY {
+ ext.args = '-r 2,4,8'
+ }
+
+}
diff --git a/tests/modules/cooler/zoomify/test.yml b/tests/modules/cooler/zoomify/test.yml
index 79a5af2c..3afdb8a6 100644
--- a/tests/modules/cooler/zoomify/test.yml
+++ b/tests/modules/cooler/zoomify/test.yml
@@ -1,8 +1,8 @@
- name: cooler zoomify test_cooler_zoomify
- command: nextflow run tests/modules/cooler/zoomify -entry test_cooler_zoomify -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cooler/zoomify -entry test_cooler_zoomify -c ./tests/config/nextflow.config -c ./tests/modules/cooler/zoomify/nextflow.config
tags:
- cooler
- cooler/zoomify
files:
- path: output/cooler/test.bedpe
- md5sum: 8d792beb609fff62b536c326661f9507
+ md5sum: 0ce5e715bfc4674cdda02f2d7e7e3170
diff --git a/tests/modules/csvtk/concat/main.nf b/tests/modules/csvtk/concat/main.nf
index 22b0205f..aee31679 100644
--- a/tests/modules/csvtk/concat/main.nf
+++ b/tests/modules/csvtk/concat/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CSVTK_CONCAT } from '../../../../modules/csvtk/concat/main.nf' addParams( options: [:] )
+include { CSVTK_CONCAT } from '../../../../modules/csvtk/concat/main.nf'
workflow test_csvtk_concat {
diff --git a/tests/modules/csvtk/concat/nextflow.config b/tests/modules/csvtk/concat/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/csvtk/concat/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/csvtk/concat/test.yml b/tests/modules/csvtk/concat/test.yml
index 0fe9c604..11a2af67 100644
--- a/tests/modules/csvtk/concat/test.yml
+++ b/tests/modules/csvtk/concat/test.yml
@@ -1,5 +1,5 @@
- name: csvtk concat
- command: nextflow run ./tests/modules/csvtk/concat -entry test_csvtk_concat -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/csvtk/concat -entry test_csvtk_concat -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/concat/nextflow.config
tags:
- csvtk
- csvtk/concat
diff --git a/tests/modules/csvtk/split/main.nf b/tests/modules/csvtk/split/main.nf
index 8dfd4053..31d24d61 100644
--- a/tests/modules/csvtk/split/main.nf
+++ b/tests/modules/csvtk/split/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CSVTK_SPLIT } from '../../../../modules/csvtk/split/main.nf' addParams( options: [args: "-C '&' --fields 'first_name' "])
+include { CSVTK_SPLIT } from '../../../../modules/csvtk/split/main.nf'
workflow test_csvtk_split_tsv {
diff --git a/tests/modules/csvtk/split/nextflow.config b/tests/modules/csvtk/split/nextflow.config
new file mode 100644
index 00000000..1dbd7615
--- /dev/null
+++ b/tests/modules/csvtk/split/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: CSVTK_SPLIT {
+ ext.args = "-C \'&\' --fields \'first_name\' "
+ }
+
+}
diff --git a/tests/modules/csvtk/split/test.yml b/tests/modules/csvtk/split/test.yml
index ade2fe48..bd13cca6 100644
--- a/tests/modules/csvtk/split/test.yml
+++ b/tests/modules/csvtk/split/test.yml
@@ -1,5 +1,5 @@
- name: csvtk split test_csvtk_split_tsv
- command: nextflow run tests/modules/csvtk/split -entry test_csvtk_split_tsv -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/csvtk/split -entry test_csvtk_split_tsv -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/split/nextflow.config
tags:
- csvtk/split
- csvtk
@@ -12,7 +12,7 @@
md5sum: 45ae6da8111096746d1736d34220a3ec
- name: csvtk split test_csvtk_split_csv
- command: nextflow run tests/modules/csvtk/split -entry test_csvtk_split_csv -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/csvtk/split -entry test_csvtk_split_csv -c ./tests/config/nextflow.config -c ./tests/modules/csvtk/split/nextflow.config
tags:
- csvtk/split
- csvtk
diff --git a/tests/modules/custom/dumpsoftwareversions/main.nf b/tests/modules/custom/dumpsoftwareversions/main.nf
index 020b19bd..95a43a82 100644
--- a/tests/modules/custom/dumpsoftwareversions/main.nf
+++ b/tests/modules/custom/dumpsoftwareversions/main.nf
@@ -2,23 +2,54 @@
nextflow.enable.dsl = 2
-include { FASTQC } from '../../../../modules/fastqc/main.nf' addParams( options: [:] )
-include { MULTIQC } from '../../../../modules/multiqc/main.nf' addParams( options: [:] )
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf' addParams( options: [publish_dir:'custom'] )
+include { FASTQC } from '../../../../modules/fastqc/main.nf'
+include { MULTIQC } from '../../../../modules/multiqc/main.nf'
+include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../../../modules/custom/dumpsoftwareversions/main.nf'
+
+workflow fastqc1 {
+ take:
+ input
+
+ main:
+ FASTQC ( input )
+
+ emit:
+ versions = FASTQC.out.versions
+}
+
+workflow fastqc2 {
+ take:
+ input
+
+ main:
+ FASTQC ( input )
+
+ emit:
+ versions = FASTQC.out.versions
+ zip = FASTQC.out.zip
+}
workflow test_custom_dumpsoftwareversions {
input = [
[ id: 'test', single_end: false ],
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
]
- FASTQC ( input )
- MULTIQC ( FASTQC.out.zip.collect { it[1] } )
+ // Using subworkflows to ensure that the script can properly handle
+ // cases where subworkflows have a module with the same name.
+ fastqc1 ( input )
+ fastqc2 ( input )
+ MULTIQC ( fastqc2.out.zip.collect { it[1] } )
- ch_software_versions = Channel.empty()
- ch_software_versions = ch_software_versions.mix(FASTQC.out.versions)
- ch_software_versions = ch_software_versions.mix(MULTIQC.out.versions)
+ fastqc1
+ .out
+ .versions
+ .mix(fastqc2.out.versions)
+ .mix(MULTIQC.out.versions)
+ .set { ch_software_versions }
CUSTOM_DUMPSOFTWAREVERSIONS ( ch_software_versions.collectFile() )
}
diff --git a/tests/modules/custom/dumpsoftwareversions/nextflow.config b/tests/modules/custom/dumpsoftwareversions/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/custom/dumpsoftwareversions/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/custom/dumpsoftwareversions/test.yml b/tests/modules/custom/dumpsoftwareversions/test.yml
index 1815c0ba..363a1218 100644
--- a/tests/modules/custom/dumpsoftwareversions/test.yml
+++ b/tests/modules/custom/dumpsoftwareversions/test.yml
@@ -1,8 +1,14 @@
- name: custom dumpsoftwareversions
- command: nextflow run ./tests/modules/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/custom/dumpsoftwareversions -entry test_custom_dumpsoftwareversions -c ./tests/config/nextflow.config -c ./tests/modules/custom/dumpsoftwareversions/nextflow.config
tags:
- custom
- custom/dumpsoftwareversions
files:
- path: output/custom/software_versions.yml
+ contains:
+ - FASTQC
+ - MULTIQC
+ must_not_contain:
+ - fastqc1
+ - fastqc2
- path: output/custom/software_versions_mqc.yml
diff --git a/tests/modules/custom/getchromsizes/main.nf b/tests/modules/custom/getchromsizes/main.nf
index 503668ec..b4f9fb9f 100644
--- a/tests/modules/custom/getchromsizes/main.nf
+++ b/tests/modules/custom/getchromsizes/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CUSTOM_GETCHROMSIZES } from '../../../../modules/custom/getchromsizes/main.nf' addParams( options: [:] )
+include { CUSTOM_GETCHROMSIZES } from '../../../../modules/custom/getchromsizes/main.nf'
workflow test_custom_getchromsizes {
diff --git a/tests/modules/custom/getchromsizes/nextflow.config b/tests/modules/custom/getchromsizes/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/custom/getchromsizes/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/custom/getchromsizes/test.yml b/tests/modules/custom/getchromsizes/test.yml
index 1265f478..9a770ad4 100644
--- a/tests/modules/custom/getchromsizes/test.yml
+++ b/tests/modules/custom/getchromsizes/test.yml
@@ -1,5 +1,5 @@
- name: custom getchromsizes
- command: nextflow run ./tests/modules/custom/getchromsizes -entry test_custom_getchromsizes -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/custom/getchromsizes -entry test_custom_getchromsizes -c ./tests/config/nextflow.config -c ./tests/modules/custom/getchromsizes/nextflow.config
tags:
- custom
- custom/getchromsizes
diff --git a/tests/modules/cutadapt/main.nf b/tests/modules/cutadapt/main.nf
index 8e060398..a47feebb 100644
--- a/tests/modules/cutadapt/main.nf
+++ b/tests/modules/cutadapt/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { CUTADAPT } from '../../../modules/cutadapt/main.nf' addParams( options: [ args:'-q 25' ] )
+include { CUTADAPT } from '../../../modules/cutadapt/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/cutadapt/nextflow.config b/tests/modules/cutadapt/nextflow.config
new file mode 100644
index 00000000..2af532cc
--- /dev/null
+++ b/tests/modules/cutadapt/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: CUTADAPT {
+ ext.args = '-q 25'
+ }
+
+}
diff --git a/tests/modules/cutadapt/test.yml b/tests/modules/cutadapt/test.yml
index 40710dc5..6fa0eb4f 100644
--- a/tests/modules/cutadapt/test.yml
+++ b/tests/modules/cutadapt/test.yml
@@ -1,5 +1,5 @@
- name: cutadapt single-end
- command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cutadapt/nextflow.config
tags:
- cutadapt
files:
@@ -7,7 +7,7 @@
- path: ./output/cutadapt/test.trim.fastq.gz
- name: cutadapt paired-end
- command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/cutadapt -entry test_cutadapt_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cutadapt/nextflow.config
tags:
- cutadapt
files:
diff --git a/tests/modules/damageprofiler/main.nf b/tests/modules/damageprofiler/main.nf
index 36ae7b24..9207caf1 100644
--- a/tests/modules/damageprofiler/main.nf
+++ b/tests/modules/damageprofiler/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DAMAGEPROFILER } from '../../../modules/damageprofiler/main.nf' addParams( options: [:] )
+include { DAMAGEPROFILER } from '../../../modules/damageprofiler/main.nf'
workflow test_damageprofiler {
diff --git a/tests/modules/damageprofiler/nextflow.config b/tests/modules/damageprofiler/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/damageprofiler/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/damageprofiler/test.yml b/tests/modules/damageprofiler/test.yml
index 9ef964dc..4a560ce1 100644
--- a/tests/modules/damageprofiler/test.yml
+++ b/tests/modules/damageprofiler/test.yml
@@ -1,5 +1,5 @@
- name: damageprofiler
- command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c tests/config/nextflow.config -dump-channels
+ command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
tags:
- damageprofiler
files:
@@ -36,7 +36,7 @@
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
- name: damageprofiler_reference
- command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c tests/config/nextflow.config -dump-channels
+ command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
tags:
- damageprofiler
files:
@@ -73,7 +73,7 @@
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
- name: damageprofiler_specieslist
- command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c tests/config/nextflow.config -dump-channels
+ command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
tags:
- damageprofiler
files:
diff --git a/tests/modules/dastool/dastool/main.nf b/tests/modules/dastool/dastool/main.nf
index 31c32ef4..f6f6becf 100644
--- a/tests/modules/dastool/dastool/main.nf
+++ b/tests/modules/dastool/dastool/main.nf
@@ -1,10 +1,10 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
-include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' addParams( options: [args: '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'] )
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' addParams( options: [:] )
-include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' addParams( options: [:] )
-include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf' addParams( options: [args: '--score_threshold 0 --debug'] )
+include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
+include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf'
+include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf'
workflow test_dastool_dastool {
diff --git a/tests/modules/dastool/dastool/nextflow.config b/tests/modules/dastool/dastool/nextflow.config
new file mode 100644
index 00000000..e306b4b4
--- /dev/null
+++ b/tests/modules/dastool/dastool/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: METABAT2_METABAT2 {
+ ext.args = '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'
+ }
+
+ withName: DASTOOL_DASTOOL {
+ ext.args = '--score_threshold 0 --debug'
+ }
+
+}
diff --git a/tests/modules/dastool/dastool/test.yml b/tests/modules/dastool/dastool/test.yml
index eff02f96..e2161890 100644
--- a/tests/modules/dastool/dastool/test.yml
+++ b/tests/modules/dastool/dastool/test.yml
@@ -1,5 +1,5 @@
- name: dastool dastool test_dastool_dastool
- command: nextflow run tests/modules/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dastool/dastool -entry test_dastool_dastool -c ./tests/config/nextflow.config -c ./tests/modules/dastool/dastool/nextflow.config
tags:
- dastool
- dastool/dastool
diff --git a/tests/modules/dastool/scaffolds2bin/main.nf b/tests/modules/dastool/scaffolds2bin/main.nf
index 63ffe82a..a0cd6726 100644
--- a/tests/modules/dastool/scaffolds2bin/main.nf
+++ b/tests/modules/dastool/scaffolds2bin/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' addParams( options: [args: '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'] )
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' addParams( options: [:] )
-include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf' addParams( options: [:] )
+include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
+include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf'
workflow test_dastool_scaffolds2bin {
diff --git a/tests/modules/dastool/scaffolds2bin/nextflow.config b/tests/modules/dastool/scaffolds2bin/nextflow.config
new file mode 100644
index 00000000..83754d8b
--- /dev/null
+++ b/tests/modules/dastool/scaffolds2bin/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: METABAT2_METABAT2 {
+ ext.args = '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'
+ }
+
+}
diff --git a/tests/modules/dastool/scaffolds2bin/test.yml b/tests/modules/dastool/scaffolds2bin/test.yml
index c6e25bff..26f528c9 100644
--- a/tests/modules/dastool/scaffolds2bin/test.yml
+++ b/tests/modules/dastool/scaffolds2bin/test.yml
@@ -1,5 +1,5 @@
- name: dastool scaffolds2bin test_dastool_scaffolds2bin
- command: nextflow run tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dastool/scaffolds2bin -entry test_dastool_scaffolds2bin -c ./tests/config/nextflow.config -c ./tests/modules/dastool/scaffolds2bin/nextflow.config
tags:
- dastool
- dastool/scaffolds2bin
diff --git a/tests/modules/dedup/main.nf b/tests/modules/dedup/main.nf
index 37e8e5c2..4a397eaa 100644
--- a/tests/modules/dedup/main.nf
+++ b/tests/modules/dedup/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DEDUP } from '../../../modules/dedup/main.nf' addParams( options: [args: "-m"] )
+include { DEDUP } from '../../../modules/dedup/main.nf'
workflow test_dedup {
diff --git a/tests/modules/dedup/nextflow.config b/tests/modules/dedup/nextflow.config
new file mode 100644
index 00000000..80a42463
--- /dev/null
+++ b/tests/modules/dedup/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DEDUP {
+ ext.args = '-m'
+ }
+
+}
diff --git a/tests/modules/dedup/test.yml b/tests/modules/dedup/test.yml
index b35cfafd..077aac0d 100644
--- a/tests/modules/dedup/test.yml
+++ b/tests/modules/dedup/test.yml
@@ -1,5 +1,5 @@
- name: dedup test_dedup
- command: nextflow run tests/modules/dedup -entry test_dedup -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dedup -entry test_dedup -c ./tests/config/nextflow.config -c ./tests/modules/dedup/nextflow.config
tags:
- dedup
files:
diff --git a/tests/modules/deeptools/computematrix/main.nf b/tests/modules/deeptools/computematrix/main.nf
index 116bc851..35e49f59 100644
--- a/tests/modules/deeptools/computematrix/main.nf
+++ b/tests/modules/deeptools/computematrix/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../modules/deeptools/computematrix/main.nf' addParams( options: ['args' : 'scale-regions -b 1000'] )
+include { DEEPTOOLS_COMPUTEMATRIX } from '../../../../modules/deeptools/computematrix/main.nf'
workflow test_deeptools_computematrix {
diff --git a/tests/modules/deeptools/computematrix/nextflow.config b/tests/modules/deeptools/computematrix/nextflow.config
new file mode 100644
index 00000000..285b2165
--- /dev/null
+++ b/tests/modules/deeptools/computematrix/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DEEPTOOLS_COMPUTEMATRIX {
+ ext.args = 'scale-regions -b 1000'
+ }
+
+}
diff --git a/tests/modules/deeptools/computematrix/test.yml b/tests/modules/deeptools/computematrix/test.yml
index fb2fa9e1..88657de3 100644
--- a/tests/modules/deeptools/computematrix/test.yml
+++ b/tests/modules/deeptools/computematrix/test.yml
@@ -1,5 +1,5 @@
- name: deeptools computematrix
- command: nextflow run tests/modules/deeptools/computematrix -entry test_deeptools_computematrix -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/deeptools/computematrix -entry test_deeptools_computematrix -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/computematrix/nextflow.config
tags:
- deeptools
- deeptools/computematrix
diff --git a/tests/modules/deeptools/plotfingerprint/main.nf b/tests/modules/deeptools/plotfingerprint/main.nf
index e84adc39..bcef970e 100644
--- a/tests/modules/deeptools/plotfingerprint/main.nf
+++ b/tests/modules/deeptools/plotfingerprint/main.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
params.fragment_size = 1000
-include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../modules/deeptools/plotfingerprint/main.nf' addParams( options: [:] )
+include { DEEPTOOLS_PLOTFINGERPRINT } from '../../../../modules/deeptools/plotfingerprint/main.nf'
workflow test_deeptools_plotfingerprint {
diff --git a/tests/modules/deeptools/plotfingerprint/nextflow.config b/tests/modules/deeptools/plotfingerprint/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/deeptools/plotfingerprint/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/deeptools/plotfingerprint/test.yml b/tests/modules/deeptools/plotfingerprint/test.yml
index b7803a6e..11d4ae7b 100644
--- a/tests/modules/deeptools/plotfingerprint/test.yml
+++ b/tests/modules/deeptools/plotfingerprint/test.yml
@@ -1,5 +1,5 @@
- name: deeptools plotfingerprint
- command: nextflow run tests/modules/deeptools/plotfingerprint -entry test_deeptools_plotfingerprint -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/deeptools/plotfingerprint -entry test_deeptools_plotfingerprint -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotfingerprint/nextflow.config
tags:
- deeptools
- deeptools/plotfingerprint
diff --git a/tests/modules/deeptools/plotheatmap/main.nf b/tests/modules/deeptools/plotheatmap/main.nf
index 93e7d373..86005b2c 100644
--- a/tests/modules/deeptools/plotheatmap/main.nf
+++ b/tests/modules/deeptools/plotheatmap/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DEEPTOOLS_PLOTHEATMAP } from '../../../../modules/deeptools/plotheatmap/main.nf' addParams( options: [:] )
+include { DEEPTOOLS_PLOTHEATMAP } from '../../../../modules/deeptools/plotheatmap/main.nf'
workflow test_deeptools_plotheatmap {
diff --git a/tests/modules/deeptools/plotheatmap/nextflow.config b/tests/modules/deeptools/plotheatmap/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/deeptools/plotheatmap/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/deeptools/plotheatmap/test.yml b/tests/modules/deeptools/plotheatmap/test.yml
index 641d5121..9273f840 100644
--- a/tests/modules/deeptools/plotheatmap/test.yml
+++ b/tests/modules/deeptools/plotheatmap/test.yml
@@ -1,5 +1,5 @@
- name: deeptools plotheatmap
- command: nextflow run tests/modules/deeptools/plotheatmap -entry test_deeptools_plotheatmap -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/deeptools/plotheatmap -entry test_deeptools_plotheatmap -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotheatmap/nextflow.config
tags:
- deeptools
- deeptools/plotheatmap
diff --git a/tests/modules/deeptools/plotprofile/main.nf b/tests/modules/deeptools/plotprofile/main.nf
index ac91f0c5..63ee47cd 100644
--- a/tests/modules/deeptools/plotprofile/main.nf
+++ b/tests/modules/deeptools/plotprofile/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DEEPTOOLS_PLOTPROFILE } from '../../../../modules/deeptools/plotprofile/main.nf' addParams( options: [:] )
+include { DEEPTOOLS_PLOTPROFILE } from '../../../../modules/deeptools/plotprofile/main.nf'
workflow test_deeptools_plotprofile {
diff --git a/tests/modules/deeptools/plotprofile/nextflow.config b/tests/modules/deeptools/plotprofile/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/deeptools/plotprofile/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/deeptools/plotprofile/test.yml b/tests/modules/deeptools/plotprofile/test.yml
index efe02ce5..4b6c5b9a 100644
--- a/tests/modules/deeptools/plotprofile/test.yml
+++ b/tests/modules/deeptools/plotprofile/test.yml
@@ -1,5 +1,5 @@
- name: deeptools plotprofile
- command: nextflow run tests/modules/deeptools/plotprofile -entry test_deeptools_plotprofile -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/deeptools/plotprofile -entry test_deeptools_plotprofile -c ./tests/config/nextflow.config -c ./tests/modules/deeptools/plotprofile/nextflow.config
tags:
- deeptools
- deeptools/plotprofile
diff --git a/tests/modules/delly/call/main.nf b/tests/modules/delly/call/main.nf
index f41dda95..f4583e05 100644
--- a/tests/modules/delly/call/main.nf
+++ b/tests/modules/delly/call/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DELLY_CALL } from '../../../../modules/delly/call/main.nf' addParams( options: [:] )
+include { DELLY_CALL } from '../../../../modules/delly/call/main.nf'
workflow test_delly_call {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/delly/call/nextflow.config b/tests/modules/delly/call/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/delly/call/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/delly/call/test.yml b/tests/modules/delly/call/test.yml
index d8750892..a770d213 100644
--- a/tests/modules/delly/call/test.yml
+++ b/tests/modules/delly/call/test.yml
@@ -1,10 +1,9 @@
- name: delly call test_delly_call
- command: nextflow run tests/modules/delly/call -entry test_delly_call -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/delly/call -entry test_delly_call -c ./tests/config/nextflow.config -c ./tests/modules/delly/call/nextflow.config
tags:
- delly
- delly/call
files:
- path: output/delly/test.bcf
- md5sum: 360c1bf6867f33bd2a868ddfb4d957fc
- path: output/delly/test.bcf.csi
md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index ab131a86..87d05bf9 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' addParams( options: [:] )
-include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf' addParams( options: [ suffix: '.diamond_blastp' ] )
+include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
+include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf'
workflow test_diamond_blastp {
diff --git a/tests/modules/diamond/blastp/nextflow.config b/tests/modules/diamond/blastp/nextflow.config
new file mode 100644
index 00000000..d1222d49
--- /dev/null
+++ b/tests/modules/diamond/blastp/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DIAMOND_BLASTP {
+ ext.suffix = '.diamond_blastp'
+ }
+
+}
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index ae62ea51..673563cb 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -1,5 +1,5 @@
- name: diamond blastp
- command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastp/nextflow.config
tags:
- diamond
- diamond/blastp
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index c0e437d7..77eb08ea 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' addParams( options: [:] )
-include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf' addParams( options: [ suffix: '.diamond_blastx' ] )
+include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
+include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
workflow test_diamond_blastx {
diff --git a/tests/modules/diamond/blastx/nextflow.config b/tests/modules/diamond/blastx/nextflow.config
new file mode 100644
index 00000000..83169455
--- /dev/null
+++ b/tests/modules/diamond/blastx/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DIAMOND_BLASTX {
+ ext.suffix = '.diamond_blastx'
+ }
+
+}
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index 91a6eb4f..ee94802f 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -1,5 +1,5 @@
- name: diamond blastx
- command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
tags:
- diamond
- diamond/blastx
diff --git a/tests/modules/diamond/makedb/main.nf b/tests/modules/diamond/makedb/main.nf
index bcd7691e..70982ae9 100644
--- a/tests/modules/diamond/makedb/main.nf
+++ b/tests/modules/diamond/makedb/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf' addParams( options: [:] )
+include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
workflow test_diamond_makedb {
diff --git a/tests/modules/diamond/makedb/nextflow.config b/tests/modules/diamond/makedb/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/diamond/makedb/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/diamond/makedb/test.yml b/tests/modules/diamond/makedb/test.yml
index 335b571f..c8f2d79e 100644
--- a/tests/modules/diamond/makedb/test.yml
+++ b/tests/modules/diamond/makedb/test.yml
@@ -1,5 +1,5 @@
- name: diamond makedb test_diamond_makedb
- command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config -c ./tests/modules/diamond/makedb/nextflow.config
tags:
- diamond
- diamond/makedb
diff --git a/tests/modules/dragonflye/main.nf b/tests/modules/dragonflye/main.nf
index 4d3ac6e5..3d59bb21 100644
--- a/tests/modules/dragonflye/main.nf
+++ b/tests/modules/dragonflye/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { DRAGONFLYE } from '../../../modules/dragonflye/main.nf' addParams( options: [args: '--assembler miniasm --gsize 5000000'] )
-include { DRAGONFLYE as DRAGONFLYE_RAVEN } from '../../../modules/dragonflye/main.nf' addParams( options: [args: '--assembler raven --gsize 5000000'] )
+include { DRAGONFLYE } from '../../../modules/dragonflye/main.nf'
+include { DRAGONFLYE as DRAGONFLYE_RAVEN } from '../../../modules/dragonflye/main.nf'
workflow test_dragonflye {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/dragonflye/nextflow.config b/tests/modules/dragonflye/nextflow.config
new file mode 100644
index 00000000..fea43da4
--- /dev/null
+++ b/tests/modules/dragonflye/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DRAGONFLYE {
+ ext.args = '--assembler miniasm --gsize 5000000'
+ }
+
+ withName: DRAGONFLYE_RAVEN {
+ ext.args = '--assembler raven --gsize 5000000'
+ }
+
+}
diff --git a/tests/modules/dragonflye/test.yml b/tests/modules/dragonflye/test.yml
index fe6283c0..ef9121ba 100644
--- a/tests/modules/dragonflye/test.yml
+++ b/tests/modules/dragonflye/test.yml
@@ -1,5 +1,5 @@
- name: dragonflye with miniasm
- command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye -c ./tests/config/nextflow.config -c ./tests/modules/dragonflye/nextflow.config
tags:
- dragonflye
files:
@@ -12,7 +12,7 @@
- path: output/dragonflye/dragonflye.log
- name: dragonflye with raven
- command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye_raven -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dragonflye -entry test_dragonflye_raven -c ./tests/config/nextflow.config -c ./tests/modules/dragonflye/nextflow.config
tags:
- dragonflye
files:
diff --git a/tests/modules/dshbio/exportsegments/main.nf b/tests/modules/dshbio/exportsegments/main.nf
index 6eef1046..c213dc54 100644
--- a/tests/modules/dshbio/exportsegments/main.nf
+++ b/tests/modules/dshbio/exportsegments/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DSHBIO_EXPORTSEGMENTS } from '../../../../modules/dshbio/exportsegments/main.nf' addParams( options: [:] )
+include { DSHBIO_EXPORTSEGMENTS } from '../../../../modules/dshbio/exportsegments/main.nf'
workflow test_dshbio_exportsegments {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/dshbio/exportsegments/nextflow.config b/tests/modules/dshbio/exportsegments/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/dshbio/exportsegments/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/dshbio/exportsegments/test.yml b/tests/modules/dshbio/exportsegments/test.yml
index 453e1cba..c811df03 100644
--- a/tests/modules/dshbio/exportsegments/test.yml
+++ b/tests/modules/dshbio/exportsegments/test.yml
@@ -1,5 +1,5 @@
- name: dshbio exportsegments
- command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
tags:
- dshbio
- dshbio/exportsegments
diff --git a/tests/modules/dshbio/filterbed/main.nf b/tests/modules/dshbio/filterbed/main.nf
index 722c88d2..454a03be 100644
--- a/tests/modules/dshbio/filterbed/main.nf
+++ b/tests/modules/dshbio/filterbed/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DSHBIO_FILTERBED } from '../../../../modules/dshbio/filterbed/main.nf' addParams( options: [suffix: '.filtered', args: '--range chr1:0-1000'] )
+include { DSHBIO_FILTERBED } from '../../../../modules/dshbio/filterbed/main.nf'
workflow test_dshbio_filterbed {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/dshbio/filterbed/nextflow.config b/tests/modules/dshbio/filterbed/nextflow.config
new file mode 100644
index 00000000..2f1e5ab9
--- /dev/null
+++ b/tests/modules/dshbio/filterbed/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DSHBIO_FILTERBED {
+ ext.args = '--range chr1:0-1000'
+ ext.suffix = '.filtered'
+ }
+}
diff --git a/tests/modules/dshbio/filterbed/test.yml b/tests/modules/dshbio/filterbed/test.yml
index ad1cde66..278fd5a3 100644
--- a/tests/modules/dshbio/filterbed/test.yml
+++ b/tests/modules/dshbio/filterbed/test.yml
@@ -1,5 +1,5 @@
- name: dshbio filterbed
- command: nextflow run ./tests/modules/dshbio/filterbed -entry test_dshbio_filterbed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dshbio/filterbed -entry test_dshbio_filterbed -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/filterbed/nextflow.config
tags:
- dshbio
- dshbio/filterbed
diff --git a/tests/modules/dshbio/filtergff3/main.nf b/tests/modules/dshbio/filtergff3/main.nf
index 3156d091..7c803781 100644
--- a/tests/modules/dshbio/filtergff3/main.nf
+++ b/tests/modules/dshbio/filtergff3/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DSHBIO_FILTERGFF3 } from '../../../../modules/dshbio/filtergff3/main.nf' addParams( options: [suffix: '.filtered', args: '--range MT192765.1:0-1000'] )
+include { DSHBIO_FILTERGFF3 } from '../../../../modules/dshbio/filtergff3/main.nf'
workflow test_dshbio_filtergff3 {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/dshbio/filtergff3/nextflow.config b/tests/modules/dshbio/filtergff3/nextflow.config
new file mode 100644
index 00000000..c4b75eaf
--- /dev/null
+++ b/tests/modules/dshbio/filtergff3/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DSHBIO_FILTERGFF3 {
+ ext.args = '--range MT192765.1:0-1000'
+ ext.suffix = '.filtered'
+ }
+
+}
diff --git a/tests/modules/dshbio/filtergff3/test.yml b/tests/modules/dshbio/filtergff3/test.yml
index 95d1b446..43238333 100644
--- a/tests/modules/dshbio/filtergff3/test.yml
+++ b/tests/modules/dshbio/filtergff3/test.yml
@@ -1,5 +1,5 @@
- name: dshbio filtergff3
- command: nextflow run ./tests/modules/dshbio/filtergff3 -entry test_dshbio_filtergff3 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dshbio/filtergff3 -entry test_dshbio_filtergff3 -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/filtergff3/nextflow.config
tags:
- dshbio
- dshbio/filtergff3
diff --git a/tests/modules/dshbio/splitbed/main.nf b/tests/modules/dshbio/splitbed/main.nf
index d7f3d004..517baad0 100644
--- a/tests/modules/dshbio/splitbed/main.nf
+++ b/tests/modules/dshbio/splitbed/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DSHBIO_SPLITBED } from '../../../../modules/dshbio/splitbed/main.nf' addParams( options: [suffix: '.', args: '--records 2'] )
+include { DSHBIO_SPLITBED } from '../../../../modules/dshbio/splitbed/main.nf'
workflow test_dshbio_splitbed {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/dshbio/splitbed/nextflow.config b/tests/modules/dshbio/splitbed/nextflow.config
new file mode 100644
index 00000000..4369c509
--- /dev/null
+++ b/tests/modules/dshbio/splitbed/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DSHBIO_SPLITBED {
+ ext.suffix = '.'
+ ext.args = '--records 2'
+ }
+
+}
diff --git a/tests/modules/dshbio/splitbed/test.yml b/tests/modules/dshbio/splitbed/test.yml
index 04f5b150..ab14648e 100644
--- a/tests/modules/dshbio/splitbed/test.yml
+++ b/tests/modules/dshbio/splitbed/test.yml
@@ -1,5 +1,5 @@
- name: dshbio splitbed
- command: nextflow run ./tests/modules/dshbio/splitbed -entry test_dshbio_splitbed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dshbio/splitbed -entry test_dshbio_splitbed -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/splitbed/nextflow.config
tags:
- dshbio
- dshbio/splitbed
diff --git a/tests/modules/dshbio/splitgff3/main.nf b/tests/modules/dshbio/splitgff3/main.nf
index dd58201a..03aa5394 100644
--- a/tests/modules/dshbio/splitgff3/main.nf
+++ b/tests/modules/dshbio/splitgff3/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { DSHBIO_SPLITGFF3 } from '../../../../modules/dshbio/splitgff3/main.nf' addParams( options: [suffix: '.', args: '--records 15'] )
+include { DSHBIO_SPLITGFF3 } from '../../../../modules/dshbio/splitgff3/main.nf'
workflow test_dshbio_splitgff3 {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/dshbio/splitgff3/nextflow.config b/tests/modules/dshbio/splitgff3/nextflow.config
new file mode 100644
index 00000000..e31f8e13
--- /dev/null
+++ b/tests/modules/dshbio/splitgff3/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: DSHBIO_SPLITGFF3 {
+ ext.suffix = '.'
+ ext.args = '--records 15'
+ }
+
+}
diff --git a/tests/modules/dshbio/splitgff3/test.yml b/tests/modules/dshbio/splitgff3/test.yml
index fe5b1bed..6087ce11 100644
--- a/tests/modules/dshbio/splitgff3/test.yml
+++ b/tests/modules/dshbio/splitgff3/test.yml
@@ -1,5 +1,5 @@
- name: dshbio splitgff3
- command: nextflow run ./tests/modules/dshbio/splitgff3 -entry test_dshbio_splitgff3 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/dshbio/splitgff3 -entry test_dshbio_splitgff3 -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/splitgff3/nextflow.config
tags:
- dshbio
- dshbio/splitgff3
diff --git a/tests/modules/ectyper/main.nf b/tests/modules/ectyper/main.nf
index 123df68d..dd359fa2 100644
--- a/tests/modules/ectyper/main.nf
+++ b/tests/modules/ectyper/main.nf
@@ -2,12 +2,14 @@
nextflow.enable.dsl = 2
-include { ECTYPER } from '../../../modules/ectyper/main.nf' addParams( options: [:] )
+include { ECTYPER } from '../../../modules/ectyper/main.nf'
workflow test_ectyper {
-
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+ ]
ECTYPER ( input )
}
diff --git a/tests/modules/ectyper/nextflow.config b/tests/modules/ectyper/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ectyper/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ectyper/test.yml b/tests/modules/ectyper/test.yml
index c6f4c668..4f909bd9 100644
--- a/tests/modules/ectyper/test.yml
+++ b/tests/modules/ectyper/test.yml
@@ -1,5 +1,5 @@
- name: ectyper test_ectyper
- command: nextflow run tests/modules/ectyper -entry test_ectyper -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ectyper -entry test_ectyper -c ./tests/config/nextflow.config -c ./tests/modules/ectyper/nextflow.config
tags:
- ectyper
files:
diff --git a/tests/modules/emmtyper/main.nf b/tests/modules/emmtyper/main.nf
index 9f2181a8..ee96fc32 100644
--- a/tests/modules/emmtyper/main.nf
+++ b/tests/modules/emmtyper/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { EMMTYPER } from '../../../modules/emmtyper/main.nf' addParams( options: [:] )
+include { EMMTYPER } from '../../../modules/emmtyper/main.nf'
workflow test_emmtyper {
diff --git a/tests/modules/emmtyper/nextflow.config b/tests/modules/emmtyper/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/emmtyper/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/emmtyper/test.yml b/tests/modules/emmtyper/test.yml
index da59e0f1..81854eb6 100644
--- a/tests/modules/emmtyper/test.yml
+++ b/tests/modules/emmtyper/test.yml
@@ -1,5 +1,5 @@
- name: emmtyper test_emmtyper
- command: nextflow run tests/modules/emmtyper -entry test_emmtyper -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/emmtyper -entry test_emmtyper -c ./tests/config/nextflow.config -c ./tests/modules/emmtyper/nextflow.config
tags:
- emmtyper
files:
diff --git a/tests/modules/ensemblvep/main.nf b/tests/modules/ensemblvep/main.nf
index 3cbb26f1..223847c7 100644
--- a/tests/modules/ensemblvep/main.nf
+++ b/tests/modules/ensemblvep/main.nf
@@ -2,11 +2,13 @@
nextflow.enable.dsl = 2
-include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf' addParams( vep_tag: '104.3.WBcel235', use_cache: false )
+include { ENSEMBLVEP } from '../../../modules/ensemblvep/main.nf'
workflow test_ensemblvep {
- input = [ [ id:'test' ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+ ]
+
ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [] )
}
diff --git a/tests/modules/ensemblvep/nextflow.config b/tests/modules/ensemblvep/nextflow.config
new file mode 100644
index 00000000..bcca2d06
--- /dev/null
+++ b/tests/modules/ensemblvep/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: ENSEMBLVEP {
+ ext.vep_tag = '104.3.WBcel235'
+ ext.use_cache = false
+ }
+
+}
diff --git a/tests/modules/ensemblvep/test.yml b/tests/modules/ensemblvep/test.yml
index a6e33cae..42384d6e 100644
--- a/tests/modules/ensemblvep/test.yml
+++ b/tests/modules/ensemblvep/test.yml
@@ -1,5 +1,5 @@
- name: ensemblvep test_ensemblvep
- command: nextflow run tests/modules/ensemblvep -entry test_ensemblvep -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ensemblvep -entry test_ensemblvep -c ./tests/config/nextflow.config -c ./tests/modules/ensemblvep/nextflow.config
tags:
- ensemblvep
files:
diff --git a/tests/modules/expansionhunter/main.nf b/tests/modules/expansionhunter/main.nf
index a7acbff4..91faeeb8 100644
--- a/tests/modules/expansionhunter/main.nf
+++ b/tests/modules/expansionhunter/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf' addParams( options: [:] )
+include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
workflow test_expansionhunter {
diff --git a/tests/modules/expansionhunter/nextflow.config b/tests/modules/expansionhunter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/expansionhunter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/expansionhunter/test.yml b/tests/modules/expansionhunter/test.yml
index 78d5c002..19403588 100644
--- a/tests/modules/expansionhunter/test.yml
+++ b/tests/modules/expansionhunter/test.yml
@@ -1,5 +1,5 @@
- name: expansionhunter test_expansionhunter
- command: nextflow run tests/modules/expansionhunter -entry test_expansionhunter -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/expansionhunter -entry test_expansionhunter -c ./tests/config/nextflow.config -c ./tests/modules/expansionhunter/nextflow.config
tags:
- expansionhunter
files:
diff --git a/tests/modules/fargene/main.nf b/tests/modules/fargene/main.nf
index f89392ff..6600015b 100644
--- a/tests/modules/fargene/main.nf
+++ b/tests/modules/fargene/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FARGENE } from '../../../modules/fargene/main.nf' addParams( options: [:] )
+include { FARGENE } from '../../../modules/fargene/main.nf'
workflow test_fargene {
diff --git a/tests/modules/fargene/nextflow.config b/tests/modules/fargene/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fargene/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fargene/test.yml b/tests/modules/fargene/test.yml
index 3db6699c..622e44b0 100644
--- a/tests/modules/fargene/test.yml
+++ b/tests/modules/fargene/test.yml
@@ -1,5 +1,5 @@
- name: fargene
- command: nextflow run tests/modules/fargene -entry test_fargene -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fargene -entry test_fargene -c ./tests/config/nextflow.config -c ./tests/modules/fargene/nextflow.config
tags:
- fargene
files:
diff --git a/tests/modules/fastani/main.nf b/tests/modules/fastani/main.nf
index a5548e20..0395f6a9 100644
--- a/tests/modules/fastani/main.nf
+++ b/tests/modules/fastani/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FASTANI } from '../../../modules/fastani/main.nf' addParams( options: [:] )
+include { FASTANI } from '../../../modules/fastani/main.nf'
workflow test_fastani {
diff --git a/tests/modules/fastani/nextflow.config b/tests/modules/fastani/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fastani/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fastani/test.yml b/tests/modules/fastani/test.yml
index cd411d06..f3748d25 100644
--- a/tests/modules/fastani/test.yml
+++ b/tests/modules/fastani/test.yml
@@ -1,5 +1,5 @@
- name: fastani
- command: nextflow run ./tests/modules/fastani -entry test_fastani -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastani -entry test_fastani -c ./tests/config/nextflow.config -c ./tests/modules/fastani/nextflow.config
tags:
- fastani
files:
diff --git a/tests/modules/fastp/main.nf b/tests/modules/fastp/main.nf
index c8e5112f..d1540974 100644
--- a/tests/modules/fastp/main.nf
+++ b/tests/modules/fastp/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FASTP } from '../../../modules/fastp/main.nf' addParams( options: [:] )
+include { FASTP } from '../../../modules/fastp/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/fastp/nextflow.config b/tests/modules/fastp/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fastp/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fastp/test.yml b/tests/modules/fastp/test.yml
index 365ce025..cd7ddeed 100644
--- a/tests/modules/fastp/test.yml
+++ b/tests/modules/fastp/test.yml
@@ -1,5 +1,5 @@
- name: fastp test_fastp_single_end
- command: nextflow run tests/modules/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
tags:
- fastp
files:
@@ -17,7 +17,7 @@
md5sum: e0d856ebb3da9e4462c3ce9683efe01d
- name: fastp test_fastp_paired_end
- command: nextflow run tests/modules/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
tags:
- fastp
files:
@@ -38,7 +38,7 @@
md5sum: 9eff7203596580cc5e42aceab4a469df
- name: fastp test_fastp_single_end_trim_fail
- command: nextflow run tests/modules/fastp -entry test_fastp_single_end_trim_fail -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
tags:
- fastp
files:
@@ -58,7 +58,7 @@
md5sum: de315d397c994d8e66bafc7a8dc11070
- name: fastp test_fastp_paired_end_trim_fail
- command: nextflow run tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
tags:
- fastp
files:
@@ -83,7 +83,7 @@
md5sum: f52309b35a7c15cbd56a9c3906ef98a5
- name: fastp test_fastp_paired_end_merged
- command: nextflow run tests/modules/fastp -entry test_fastp_paired_end_merged -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
tags:
- fastp
files:
diff --git a/tests/modules/fastqc/main.nf b/tests/modules/fastqc/main.nf
index d95befec..f7db9b7c 100644
--- a/tests/modules/fastqc/main.nf
+++ b/tests/modules/fastqc/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FASTQC } from '../../../modules/fastqc/main.nf' addParams( options: [:] )
+include { FASTQC } from '../../../modules/fastqc/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/fastqc/nextflow.config b/tests/modules/fastqc/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fastqc/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fastqc/test.yml b/tests/modules/fastqc/test.yml
index 794e63fe..fa830cbc 100644
--- a/tests/modules/fastqc/test.yml
+++ b/tests/modules/fastqc/test.yml
@@ -1,5 +1,5 @@
- name: fastqc single-end
- command: nextflow run ./tests/modules/fastqc/ -entry test_fastqc_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastqc/ -entry test_fastqc_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastqc/nextflow.config -c ./tests/modules/fastqc/nextflow.config
tags:
- fastqc
files:
@@ -7,7 +7,7 @@
- path: ./output/fastqc/test_fastqc.zip
- name: fastqc paired-end
- command: nextflow run ./tests/modules/fastqc/ -entry test_fastqc_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastqc/ -entry test_fastqc_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastqc/nextflow.config -c ./tests/modules/fastqc/nextflow.config
tags:
- fastqc
files:
diff --git a/tests/modules/fastqscan/main.nf b/tests/modules/fastqscan/main.nf
index 5fd824f6..b9a321fe 100644
--- a/tests/modules/fastqscan/main.nf
+++ b/tests/modules/fastqscan/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FASTQSCAN } from '../../../modules/fastqscan/main.nf' addParams( options: [ args: "-g 30000"] )
+include { FASTQSCAN } from '../../../modules/fastqscan/main.nf'
workflow test_fastqscan {
diff --git a/tests/modules/fastqscan/nextflow.config b/tests/modules/fastqscan/nextflow.config
new file mode 100644
index 00000000..f688ecb6
--- /dev/null
+++ b/tests/modules/fastqscan/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: FASTQSCAN {
+ ext.args = '-g 30000'
+ }
+
+}
diff --git a/tests/modules/fastqscan/test.yml b/tests/modules/fastqscan/test.yml
index 80bcbc47..d538804c 100644
--- a/tests/modules/fastqscan/test.yml
+++ b/tests/modules/fastqscan/test.yml
@@ -1,5 +1,5 @@
- name: fastqscan test_fastqscan
- command: nextflow run tests/modules/fastqscan -entry test_fastqscan -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fastqscan -entry test_fastqscan -c ./tests/config/nextflow.config -c ./tests/modules/fastqscan/nextflow.config
tags:
- fastqscan
files:
diff --git a/tests/modules/fasttree/main.nf b/tests/modules/fasttree/main.nf
index 109aaa77..e33228a9 100644
--- a/tests/modules/fasttree/main.nf
+++ b/tests/modules/fasttree/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FASTTREE } from '../../../modules/fasttree/main.nf' addParams( options: [:] )
+include { FASTTREE } from '../../../modules/fasttree/main.nf'
workflow test_fasttree {
diff --git a/tests/modules/fasttree/nextflow.config b/tests/modules/fasttree/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fasttree/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fasttree/test.yml b/tests/modules/fasttree/test.yml
index b30590c7..7e344cff 100644
--- a/tests/modules/fasttree/test.yml
+++ b/tests/modules/fasttree/test.yml
@@ -1,5 +1,5 @@
- name: fasttree
- command: nextflow run ./tests/modules/fasttree -entry test_fasttree -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fasttree -entry test_fasttree -c ./tests/config/nextflow.config -c ./tests/modules/fasttree/nextflow.config
tags:
- fasttree
files:
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/main.nf b/tests/modules/fgbio/callmolecularconsensusreads/main.nf
index 8ce34eca..e31fdf39 100644
--- a/tests/modules/fgbio/callmolecularconsensusreads/main.nf
+++ b/tests/modules/fgbio/callmolecularconsensusreads/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf' addParams( options: [args: '-s TemplateCoordinate', suffix: '_out'] )
-include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../modules/fgbio/callmolecularconsensusreads/main.nf' addParams( options: [args: '-M 1', suffix: '_molreads'] )
+include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf'
+include { FGBIO_CALLMOLECULARCONSENSUSREADS } from '../../../../modules/fgbio/callmolecularconsensusreads/main.nf'
workflow test_fgbio_callmolecularconsensusreads {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config b/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config
new file mode 100644
index 00000000..0a266da9
--- /dev/null
+++ b/tests/modules/fgbio/callmolecularconsensusreads/nextflow.config
@@ -0,0 +1,15 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: FGBIO_SORTBAM {
+ ext.args = '-s TemplateCoordinate'
+ ext.suffix = '_out'
+ }
+
+ withName: FGBIO_CALLMOLECULARCONSENSUSREADS {
+ ext.args = '-M 1'
+ ext.suffix = '_molreads'
+ }
+
+}
diff --git a/tests/modules/fgbio/callmolecularconsensusreads/test.yml b/tests/modules/fgbio/callmolecularconsensusreads/test.yml
index ac53957c..5e26cd01 100644
--- a/tests/modules/fgbio/callmolecularconsensusreads/test.yml
+++ b/tests/modules/fgbio/callmolecularconsensusreads/test.yml
@@ -1,5 +1,5 @@
- name: fgbio callmolecularconsensusreads
- command: nextflow run tests/modules/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fgbio/callmolecularconsensusreads -entry test_fgbio_callmolecularconsensusreads -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/callmolecularconsensusreads/nextflow.config
tags:
- fgbio
- fgbio/callmolecularconsensusreads
diff --git a/tests/modules/fgbio/fastqtobam/main.nf b/tests/modules/fgbio/fastqtobam/main.nf
index ce2f7efc..f01a17fa 100644
--- a/tests/modules/fgbio/fastqtobam/main.nf
+++ b/tests/modules/fgbio/fastqtobam/main.nf
@@ -1,16 +1,19 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
-params.read_structure = "+T 12M11S+T"
-include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf' addParams( options: [:] )
+include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf'
workflow test_fgbio_fastqtobam {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
+ read_structure = "+T 12M11S+T"
- FGBIO_FASTQTOBAM ( input, "${params.read_structure}" )
+ FGBIO_FASTQTOBAM ( input, read_structure )
}
diff --git a/tests/modules/fgbio/fastqtobam/nextflow.config b/tests/modules/fgbio/fastqtobam/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fgbio/fastqtobam/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fgbio/fastqtobam/test.yml b/tests/modules/fgbio/fastqtobam/test.yml
index 6f2554e9..ab73f425 100644
--- a/tests/modules/fgbio/fastqtobam/test.yml
+++ b/tests/modules/fgbio/fastqtobam/test.yml
@@ -1,10 +1,8 @@
- name: fgbio fastqtobam test_fgbio_fastqtobam
- command: nextflow run tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
tags:
- fgbio/fastqtobam
- fgbio
files:
- path: output/fgbio/test_umi_converted.bam
md5sum: 9510735554e5eff29244077a72075fb6
- - path: output/fgbio/versions.yml
- md5sum: 524815093b96759060d0d800fc6a3f25
diff --git a/tests/modules/fgbio/groupreadsbyumi/main.nf b/tests/modules/fgbio/groupreadsbyumi/main.nf
index 31f55724..1d5fb474 100644
--- a/tests/modules/fgbio/groupreadsbyumi/main.nf
+++ b/tests/modules/fgbio/groupreadsbyumi/main.nf
@@ -2,13 +2,14 @@
nextflow.enable.dsl = 2
-include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/fgbio/groupreadsbyumi/main.nf' addParams( options: [:] )
+include { FGBIO_GROUPREADSBYUMI } from '../../../../modules/fgbio/groupreadsbyumi/main.nf'
workflow test_fgbio_groupreadsbyumi {
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_tagged_bam'], checkIfExists: true) ]
-
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_umi_unsorted_tagged_bam'], checkIfExists: true)
+ ]
strategy = "Adjacency"
FGBIO_GROUPREADSBYUMI ( input, strategy )
diff --git a/tests/modules/fgbio/groupreadsbyumi/nextflow.config b/tests/modules/fgbio/groupreadsbyumi/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fgbio/groupreadsbyumi/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fgbio/groupreadsbyumi/test.yml b/tests/modules/fgbio/groupreadsbyumi/test.yml
index ce70f129..c1cfd4f0 100644
--- a/tests/modules/fgbio/groupreadsbyumi/test.yml
+++ b/tests/modules/fgbio/groupreadsbyumi/test.yml
@@ -1,5 +1,5 @@
- name: fgbio groupreadsbyumi test_fgbio_groupreadsbyumi
- command: nextflow run tests/modules/fgbio/groupreadsbyumi -entry test_fgbio_groupreadsbyumi -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fgbio/groupreadsbyumi -entry test_fgbio_groupreadsbyumi -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/groupreadsbyumi/nextflow.config
tags:
- fgbio
- fgbio/groupreadsbyumi
diff --git a/tests/modules/fgbio/sortbam/main.nf b/tests/modules/fgbio/sortbam/main.nf
index 65bea1d7..ada99d0f 100644
--- a/tests/modules/fgbio/sortbam/main.nf
+++ b/tests/modules/fgbio/sortbam/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf' addParams( options: [:] )
+include { FGBIO_SORTBAM } from '../../../../modules/fgbio/sortbam/main.nf'
workflow test_fgbio_sortbam {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/fgbio/sortbam/nextflow.config b/tests/modules/fgbio/sortbam/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/fgbio/sortbam/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/fgbio/sortbam/test.yml b/tests/modules/fgbio/sortbam/test.yml
index 68183cd2..6789aed8 100644
--- a/tests/modules/fgbio/sortbam/test.yml
+++ b/tests/modules/fgbio/sortbam/test.yml
@@ -1,5 +1,5 @@
- name: fgbio sortbam
- command: nextflow run tests/modules/fgbio/sortbam -entry test_fgbio_sortbam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/fgbio/sortbam -entry test_fgbio_sortbam -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/sortbam/nextflow.config
tags:
- fgbio
- fgbio/sortbam
diff --git a/tests/modules/filtlong/main.nf b/tests/modules/filtlong/main.nf
index cd037623..df7892aa 100644
--- a/tests/modules/filtlong/main.nf
+++ b/tests/modules/filtlong/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FILTLONG } from '../../../modules/filtlong/main.nf' addParams( options: [:] )
+include { FILTLONG } from '../../../modules/filtlong/main.nf'
workflow test_filtlong {
diff --git a/tests/modules/filtlong/nextflow.config b/tests/modules/filtlong/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/filtlong/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/filtlong/test.yml b/tests/modules/filtlong/test.yml
index 30779d45..dc5fa5a9 100644
--- a/tests/modules/filtlong/test.yml
+++ b/tests/modules/filtlong/test.yml
@@ -1,5 +1,5 @@
- name: filtlong test_filtlong
- command: nextflow run tests/modules/filtlong -entry test_filtlong -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
tags:
- filtlong
files:
@@ -7,7 +7,7 @@
md5sum: 7029066c27ac6f5ef18d660d5741979a
- name: filtlong test_filtlong_illumina_se
- command: nextflow run tests/modules/filtlong -entry test_filtlong_illumina_se -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
tags:
- filtlong
files:
@@ -15,7 +15,7 @@
md5sum: 7029066c27ac6f5ef18d660d5741979a
- name: filtlong test_filtlong_illumina_pe
- command: nextflow run tests/modules/filtlong -entry test_filtlong_illumina_pe -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
tags:
- filtlong
files:
diff --git a/tests/modules/flash/main.nf b/tests/modules/flash/main.nf
index 2128650d..4afcb8fc 100644
--- a/tests/modules/flash/main.nf
+++ b/tests/modules/flash/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FLASH } from '../../../modules/flash/main.nf' addParams( options: [args:'-m 20 -M 100'] )
+include { FLASH } from '../../../modules/flash/main.nf'
workflow test_flash {
input = [
diff --git a/tests/modules/flash/nextflow.config b/tests/modules/flash/nextflow.config
new file mode 100644
index 00000000..2845f9d9
--- /dev/null
+++ b/tests/modules/flash/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: FLASH {
+ ext.args = '-m 20 -M 100'
+ }
+
+}
diff --git a/tests/modules/flash/test.yml b/tests/modules/flash/test.yml
index 31cdaeff..e5ed49ca 100644
--- a/tests/modules/flash/test.yml
+++ b/tests/modules/flash/test.yml
@@ -1,5 +1,5 @@
- name: flash test_flash
- command: nextflow run tests/modules/flash -entry test_flash -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/flash -entry test_flash -c ./tests/config/nextflow.config -c ./tests/modules/flash/nextflow.config
tags:
- flash
files:
diff --git a/tests/modules/freebayes/main.nf b/tests/modules/freebayes/main.nf
index c6f5641f..f8ae0ecb 100644
--- a/tests/modules/freebayes/main.nf
+++ b/tests/modules/freebayes/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { FREEBAYES } from '../../../modules/freebayes/main.nf' addParams( options: [:] )
+include { FREEBAYES } from '../../../modules/freebayes/main.nf'
workflow test_freebayes {
diff --git a/tests/modules/freebayes/nextflow.config b/tests/modules/freebayes/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/freebayes/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/freebayes/test.yml b/tests/modules/freebayes/test.yml
index 22fd0e88..c9aa78da 100644
--- a/tests/modules/freebayes/test.yml
+++ b/tests/modules/freebayes/test.yml
@@ -1,33 +1,33 @@
- name: freebayes test_freebayes
- command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
- name: freebayes test_freebayes_bed
- command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
- name: freebayes test_freebayes_cram
- command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
- name: freebayes test_freebayes_somatic
- command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
tags:
- freebayes
files:
- path: output/freebayes/test.vcf.gz
- name: freebayes test_freebayes_somatic_cram_intervals
- command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
tags:
- freebayes
files:
diff --git a/tests/modules/gatk4/applybqsr/main.nf b/tests/modules/gatk4/applybqsr/main.nf
index 80b51015..da85b11b 100644
--- a/tests/modules/gatk4/applybqsr/main.nf
+++ b/tests/modules/gatk4/applybqsr/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf' addParams( options: [:] )
+include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf'
workflow test_gatk4_applybqsr {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/applybqsr/nextflow.config b/tests/modules/gatk4/applybqsr/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/applybqsr/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml
index 02448b02..d0b07d94 100644
--- a/tests/modules/gatk4/applybqsr/test.yml
+++ b/tests/modules/gatk4/applybqsr/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 applybqsr test_gatk4_applybqsr
- command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
tags:
- gatk4/applybqsr
- gatk4
@@ -8,7 +8,7 @@
md5sum: af56f5dd81b95070079d54670507f530
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
- command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
tags:
- gatk4/applybqsr
- gatk4
@@ -17,7 +17,7 @@
md5sum: 0cbfa4be143e988d56ce741b5077510e
- name: gatk4 applybqsr test_gatk4_applybqsr_cram
- command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
tags:
- gatk4/applybqsr
- gatk4
diff --git a/tests/modules/gatk4/baserecalibrator/main.nf b/tests/modules/gatk4/baserecalibrator/main.nf
index a50c09e3..2675d04b 100644
--- a/tests/modules/gatk4/baserecalibrator/main.nf
+++ b/tests/modules/gatk4/baserecalibrator/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_BASERECALIBRATOR } from '../../../../modules/gatk4/baserecalibrator/main.nf' addParams( options: [:] )
+include { GATK4_BASERECALIBRATOR } from '../../../../modules/gatk4/baserecalibrator/main.nf'
workflow test_gatk4_baserecalibrator {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/baserecalibrator/nextflow.config b/tests/modules/gatk4/baserecalibrator/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/baserecalibrator/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/baserecalibrator/test.yml b/tests/modules/gatk4/baserecalibrator/test.yml
index a15c9ee3..163fac08 100644
--- a/tests/modules/gatk4/baserecalibrator/test.yml
+++ b/tests/modules/gatk4/baserecalibrator/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator
- command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
tags:
- gatk4
- gatk4/baserecalibrator
@@ -8,7 +8,7 @@
md5sum: e2e43abdc0c943c1a54dae816d0b9ea7
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_cram
- command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
tags:
- gatk4
- gatk4/baserecalibrator
@@ -17,7 +17,7 @@
md5sum: 35d89a3811aa31711fc9815b6b80e6ec
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
- command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
tags:
- gatk4
- gatk4/baserecalibrator
@@ -26,7 +26,7 @@
md5sum: 9ecb5f00a2229291705addc09c0ec231
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_multiple_sites
- command: nextflow run tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/baserecalibrator/nextflow.config
tags:
- gatk4
- gatk4/baserecalibrator
diff --git a/tests/modules/gatk4/bedtointervallist/main.nf b/tests/modules/gatk4/bedtointervallist/main.nf
index 1ca4be58..2dd72904 100644
--- a/tests/modules/gatk4/bedtointervallist/main.nf
+++ b/tests/modules/gatk4/bedtointervallist/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf' addParams( options: [:] )
+include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf'
workflow test_gatk4_bedtointervallist {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/bedtointervallist/nextflow.config b/tests/modules/gatk4/bedtointervallist/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/bedtointervallist/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/bedtointervallist/test.yml b/tests/modules/gatk4/bedtointervallist/test.yml
index 83c3a574..3482fa6c 100644
--- a/tests/modules/gatk4/bedtointervallist/test.yml
+++ b/tests/modules/gatk4/bedtointervallist/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 bedtointervallist test_gatk4_bedtointervallist
- command: nextflow run tests/modules/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/bedtointervallist/nextflow.config
tags:
- gatk4
- gatk4/bedtointervallist
diff --git a/tests/modules/gatk4/calculatecontamination/main.nf b/tests/modules/gatk4/calculatecontamination/main.nf
index f93f66fb..4b659ed3 100644
--- a/tests/modules/gatk4/calculatecontamination/main.nf
+++ b/tests/modules/gatk4/calculatecontamination/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/gatk4/calculatecontamination/main.nf' addParams( options: [:] )
+include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/gatk4/calculatecontamination/main.nf'
workflow test_gatk4_calculatecontamination_tumor_only {
diff --git a/tests/modules/gatk4/calculatecontamination/nextflow.config b/tests/modules/gatk4/calculatecontamination/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/calculatecontamination/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml
index 89d419e0..0c489bff 100644
--- a/tests/modules/gatk4/calculatecontamination/test.yml
+++ b/tests/modules/gatk4/calculatecontamination/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_tumor_only
- command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_tumor_only -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
tags:
- gatk4/calculatecontamination
- gatk4
@@ -8,7 +8,7 @@
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair
- command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
tags:
- gatk4/calculatecontamination
- gatk4
@@ -17,7 +17,7 @@
md5sum: 5fdcf1728cf98985ce31c038eb24e05c
- name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
- command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
tags:
- gatk4/calculatecontamination
- gatk4
diff --git a/tests/modules/gatk4/createsequencedictionary/main.nf b/tests/modules/gatk4/createsequencedictionary/main.nf
index 443d77bc..b304b043 100644
--- a/tests/modules/gatk4/createsequencedictionary/main.nf
+++ b/tests/modules/gatk4/createsequencedictionary/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../modules/gatk4/createsequencedictionary/main.nf' addParams( options: [:] )
+include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../../modules/gatk4/createsequencedictionary/main.nf'
workflow test_gatk4_createsequencedictionary {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/gatk4/createsequencedictionary/nextflow.config b/tests/modules/gatk4/createsequencedictionary/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/createsequencedictionary/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/createsequencedictionary/test.yml b/tests/modules/gatk4/createsequencedictionary/test.yml
index 7788d16a..134a9d74 100644
--- a/tests/modules/gatk4/createsequencedictionary/test.yml
+++ b/tests/modules/gatk4/createsequencedictionary/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 createsequencedictionary test_gatk4_createsequencedictionary
- command: nextflow run tests/modules/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/createsequencedictionary -entry test_gatk4_createsequencedictionary -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/createsequencedictionary/nextflow.config
tags:
- gatk4
- gatk4/createsequencedictionary
diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/main.nf b/tests/modules/gatk4/createsomaticpanelofnormals/main.nf
index 6e5366f5..5e1d1904 100644
--- a/tests/modules/gatk4/createsomaticpanelofnormals/main.nf
+++ b/tests/modules/gatk4/createsomaticpanelofnormals/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
-include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/gatk4/createsomaticpanelofnormals/main.nf' addParams( options: [suffix:'.pon'] )
+include { UNTAR } from '../../../../modules/untar/main.nf'
+include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/gatk4/createsomaticpanelofnormals/main.nf'
workflow test_gatk4_createsomaticpanelofnormals {
db = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config b/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config
new file mode 100644
index 00000000..6fda39ec
--- /dev/null
+++ b/tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_CREATESOMATICPANELOFNORMALS {
+ ext.suffix = '.pon'
+ }
+
+}
diff --git a/tests/modules/gatk4/createsomaticpanelofnormals/test.yml b/tests/modules/gatk4/createsomaticpanelofnormals/test.yml
index d71059ad..a0e2bf26 100644
--- a/tests/modules/gatk4/createsomaticpanelofnormals/test.yml
+++ b/tests/modules/gatk4/createsomaticpanelofnormals/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 createsomaticpanelofnormals test_gatk4_createsomaticpanelofnormals
- command: nextflow run tests/modules/gatk4/createsomaticpanelofnormals -entry test_gatk4_createsomaticpanelofnormals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/createsomaticpanelofnormals -entry test_gatk4_createsomaticpanelofnormals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/createsomaticpanelofnormals/nextflow.config
tags:
- gatk4
- gatk4/createsomaticpanelofnormals
diff --git a/tests/modules/gatk4/estimatelibrarycomplexity/main.nf b/tests/modules/gatk4/estimatelibrarycomplexity/main.nf
index 72772318..398a6c79 100644
--- a/tests/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ b/tests/modules/gatk4/estimatelibrarycomplexity/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/gatk4/estimatelibrarycomplexity/main.nf' addParams( options: [:] )
+include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../../modules/gatk4/estimatelibrarycomplexity/main.nf'
workflow test_gatk4_estimatelibrarycomplexity {
diff --git a/tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config b/tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/estimatelibrarycomplexity/test.yml b/tests/modules/gatk4/estimatelibrarycomplexity/test.yml
index ca949c00..a33e4ec1 100644
--- a/tests/modules/gatk4/estimatelibrarycomplexity/test.yml
+++ b/tests/modules/gatk4/estimatelibrarycomplexity/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 estimatelibrarycomplexity test_gatk4_estimatelibrarycomplexity
- command: nextflow run tests/modules/gatk4/estimatelibrarycomplexity -entry test_gatk4_estimatelibrarycomplexity -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/estimatelibrarycomplexity -entry test_gatk4_estimatelibrarycomplexity -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/estimatelibrarycomplexity/nextflow.config
tags:
- gatk4/estimatelibrarycomplexity
- gatk4
diff --git a/tests/modules/gatk4/fastqtosam/main.nf b/tests/modules/gatk4/fastqtosam/main.nf
index 64694d9f..4f53c791 100644
--- a/tests/modules/gatk4/fastqtosam/main.nf
+++ b/tests/modules/gatk4/fastqtosam/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_FASTQTOSAM } from '../../../../modules/gatk4/fastqtosam/main.nf' addParams( options: [:] )
+include { GATK4_FASTQTOSAM } from '../../../../modules/gatk4/fastqtosam/main.nf'
workflow test_gatk4_fastqtosam_single_end {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/gatk4/fastqtosam/nextflow.config b/tests/modules/gatk4/fastqtosam/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/fastqtosam/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml
index b576075a..d5d23f94 100644
--- a/tests/modules/gatk4/fastqtosam/test.yml
+++ b/tests/modules/gatk4/fastqtosam/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 fastqtosam test_gatk4_fastqtosam_single_end
- command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config
tags:
- gatk4/fastqtosam
- gatk4
@@ -8,7 +8,7 @@
md5sum: 0a0d308b219837977b8df9daa26db7de
- name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
- command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config
tags:
- gatk4
- gatk4/fastqtosam
diff --git a/tests/modules/gatk4/filtermutectcalls/main.nf b/tests/modules/gatk4/filtermutectcalls/main.nf
index 5b2938e8..fa0acff9 100644
--- a/tests/modules/gatk4/filtermutectcalls/main.nf
+++ b/tests/modules/gatk4/filtermutectcalls/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutectcalls/main.nf' addParams( options: [suffix:'.filtered'] )
+include { GATK4_FILTERMUTECTCALLS } from '../../../../modules/gatk4/filtermutectcalls/main.nf'
workflow test_gatk4_filtermutectcalls_base {
diff --git a/tests/modules/gatk4/filtermutectcalls/nextflow.config b/tests/modules/gatk4/filtermutectcalls/nextflow.config
new file mode 100644
index 00000000..c830fdc6
--- /dev/null
+++ b/tests/modules/gatk4/filtermutectcalls/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_FILTERMUTECTCALLS {
+ ext.suffix = '.filtered'
+ }
+
+}
diff --git a/tests/modules/gatk4/filtermutectcalls/test.yml b/tests/modules/gatk4/filtermutectcalls/test.yml
index d5b97d36..72504e66 100644
--- a/tests/modules/gatk4/filtermutectcalls/test.yml
+++ b/tests/modules/gatk4/filtermutectcalls/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_base
- command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_base -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
tags:
- gatk4
- gatk4/filtermutectcalls
@@ -11,7 +11,7 @@
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_with_files
- command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_with_files -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
tags:
- gatk4
- gatk4/filtermutectcalls
@@ -23,7 +23,7 @@
md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4
- name: gatk4 filtermutectcalls test_gatk4_filtermutectcalls_use_val
- command: nextflow run tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/filtermutectcalls -entry test_gatk4_filtermutectcalls_use_val -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtermutectcalls/nextflow.config
tags:
- gatk4
- gatk4/filtermutectcalls
diff --git a/tests/modules/gatk4/genomicsdbimport/main.nf b/tests/modules/gatk4/genomicsdbimport/main.nf
index aff3973d..417a08a4 100644
--- a/tests/modules/gatk4/genomicsdbimport/main.nf
+++ b/tests/modules/gatk4/genomicsdbimport/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
-include { GATK4_GENOMICSDBIMPORT } from '../../../../modules/gatk4/genomicsdbimport/main.nf' addParams( options: [:] )
+include { UNTAR } from '../../../../modules/untar/main.nf'
+include { GATK4_GENOMICSDBIMPORT } from '../../../../modules/gatk4/genomicsdbimport/main.nf'
workflow test_gatk4_genomicsdbimport_create_genomicsdb {
diff --git a/tests/modules/gatk4/genomicsdbimport/nextflow.config b/tests/modules/gatk4/genomicsdbimport/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/genomicsdbimport/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/genomicsdbimport/test.yml b/tests/modules/gatk4/genomicsdbimport/test.yml
index 5fe2b49b..94a1a35e 100644
--- a/tests/modules/gatk4/genomicsdbimport/test.yml
+++ b/tests/modules/gatk4/genomicsdbimport/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_create_genomicsdb
- command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_create_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
tags:
- gatk4/genomicsdbimport
- gatk4
@@ -20,7 +20,7 @@
md5sum: 18d3f68bd2cb6f4474990507ff95017a
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist
- command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
tags:
- gatk4/genomicsdbimport
- gatk4
@@ -29,7 +29,7 @@
md5sum: 4c85812ac15fc1cd29711a851d23c0bf
- name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_update_genomicsdb
- command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_update_genomicsdb -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
tags:
- gatk4/genomicsdbimport
- gatk4
diff --git a/tests/modules/gatk4/genotypegvcfs/main.nf b/tests/modules/gatk4/genotypegvcfs/main.nf
index 0b555180..208faf8b 100644
--- a/tests/modules/gatk4/genotypegvcfs/main.nf
+++ b/tests/modules/gatk4/genotypegvcfs/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { GATK4_GENOTYPEGVCFS } from '../../../../modules/gatk4/genotypegvcfs/main.nf' addParams( options: [suffix:'.genotyped'] )
-include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
+include { GATK4_GENOTYPEGVCFS } from '../../../../modules/gatk4/genotypegvcfs/main.nf'
+include { UNTAR } from '../../../../modules/untar/main.nf'
// Basic parameters with uncompressed VCF input
workflow test_gatk4_genotypegvcfs_vcf_input {
diff --git a/tests/modules/gatk4/genotypegvcfs/nextflow.config b/tests/modules/gatk4/genotypegvcfs/nextflow.config
new file mode 100644
index 00000000..aaa704da
--- /dev/null
+++ b/tests/modules/gatk4/genotypegvcfs/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_GENOTYPEGVCFS {
+ ext.suffix = '.genotyped'
+ }
+
+}
diff --git a/tests/modules/gatk4/genotypegvcfs/test.yml b/tests/modules/gatk4/genotypegvcfs/test.yml
index ad39a48d..45201af2 100644
--- a/tests/modules/gatk4/genotypegvcfs/test.yml
+++ b/tests/modules/gatk4/genotypegvcfs/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_vcf_input
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -8,7 +8,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -17,7 +17,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -26,7 +26,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -35,7 +35,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -44,7 +44,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -53,7 +53,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -62,7 +62,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
@@ -71,7 +71,7 @@
contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680']
- name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals
- command: nextflow run tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/genotypegvcfs -entry test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/genotypegvcfs/nextflow.config
tags:
- gatk4
- gatk4/genotypegvcfs
diff --git a/tests/modules/gatk4/getpileupsummaries/main.nf b/tests/modules/gatk4/getpileupsummaries/main.nf
index 66ee4990..52f3bdec 100644
--- a/tests/modules/gatk4/getpileupsummaries/main.nf
+++ b/tests/modules/gatk4/getpileupsummaries/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf' addParams( options: [:] )
+include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf'
workflow test_gatk4_getpileupsummaries_just_variants {
diff --git a/tests/modules/gatk4/getpileupsummaries/nextflow.config b/tests/modules/gatk4/getpileupsummaries/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/getpileupsummaries/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml
index 6c5e1f84..3211a8fe 100644
--- a/tests/modules/gatk4/getpileupsummaries/test.yml
+++ b/tests/modules/gatk4/getpileupsummaries/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants
- command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config
tags:
- gatk4
- gatk4/getpileupsummaries
@@ -8,7 +8,7 @@
md5sum: 0d19674bef2ff0700d5b02b3463dd210
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
- command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config
tags:
- gatk4
- gatk4/getpileupsummaries
diff --git a/tests/modules/gatk4/haplotypecaller/main.nf b/tests/modules/gatk4/haplotypecaller/main.nf
index fd5f30fa..dc6bec67 100644
--- a/tests/modules/gatk4/haplotypecaller/main.nf
+++ b/tests/modules/gatk4/haplotypecaller/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf' addParams( options: [:] )
+include { GATK4_HAPLOTYPECALLER } from '../../../../modules/gatk4/haplotypecaller/main.nf'
workflow test_gatk4_haplotypecaller {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/haplotypecaller/nextflow.config b/tests/modules/gatk4/haplotypecaller/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/haplotypecaller/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
index 480ff8f0..31dd23fd 100644
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ b/tests/modules/gatk4/haplotypecaller/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller
- command: nextflow run tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
tags:
- gatk4/haplotypecaller
- gatk4
@@ -8,7 +8,7 @@
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
- command: nextflow run tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
tags:
- gatk4/haplotypecaller
- gatk4
@@ -17,7 +17,7 @@
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
- command: nextflow run tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
tags:
- gatk4/haplotypecaller
- gatk4
diff --git a/tests/modules/gatk4/indexfeaturefile/main.nf b/tests/modules/gatk4/indexfeaturefile/main.nf
index e523606a..f61b57fc 100644
--- a/tests/modules/gatk4/indexfeaturefile/main.nf
+++ b/tests/modules/gatk4/indexfeaturefile/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_INDEXFEATUREFILE } from '../../../../modules/gatk4/indexfeaturefile/main.nf' addParams( options: [:] )
+include { GATK4_INDEXFEATUREFILE } from '../../../../modules/gatk4/indexfeaturefile/main.nf'
workflow test_gatk4_indexfeaturefile_bed {
diff --git a/tests/modules/gatk4/indexfeaturefile/nextflow.config b/tests/modules/gatk4/indexfeaturefile/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/indexfeaturefile/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/indexfeaturefile/test.yml b/tests/modules/gatk4/indexfeaturefile/test.yml
index 5883695a..c524e462 100644
--- a/tests/modules/gatk4/indexfeaturefile/test.yml
+++ b/tests/modules/gatk4/indexfeaturefile/test.yml
@@ -2,7 +2,7 @@
# a) the path to the file is embedded inside it,
# b) the file is binary so we can't check for text inside it.
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed
- command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
tags:
- gatk4
- gatk4/indexfeaturefile
@@ -10,7 +10,7 @@
- path: output/gatk4/genome.bed.idx
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_bed_gz
- command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_bed_gz -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
tags:
- gatk4
- gatk4/indexfeaturefile
@@ -22,7 +22,7 @@
# a) the path to the file is embedded inside it,
# b) the file is binary so we can't check for text inside it.
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
- command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
tags:
- gatk4
- gatk4/indexfeaturefile
@@ -30,7 +30,7 @@
- path: output/gatk4/test.genome.vcf.idx
- name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
- command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
tags:
- gatk4
- gatk4/indexfeaturefile
diff --git a/tests/modules/gatk4/intervallisttools/main.nf b/tests/modules/gatk4/intervallisttools/main.nf
index 59be74e8..535923fb 100644
--- a/tests/modules/gatk4/intervallisttools/main.nf
+++ b/tests/modules/gatk4/intervallisttools/main.nf
@@ -2,15 +2,17 @@
nextflow.enable.dsl = 2
-test_options = ['args': '--SCATTER_COUNT 6 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --UNIQUE true --SORT true']
-include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf' addParams( options: [:] )
-include { GATK4_INTERVALLISTTOOLS as INTERVALLISTTOOLS } from '../../../../modules/gatk4/intervallisttools/main.nf' addParams( options: test_options )
+include { GATK4_BEDTOINTERVALLIST } from '../../../../modules/gatk4/bedtointervallist/main.nf'
+include { GATK4_INTERVALLISTTOOLS } from '../../../../modules/gatk4/intervallisttools/main.nf'
workflow test_gatk4_intervallisttools {
- input = [ [ id:'test' ], [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]]
+ input = [
+ [ id:'test' ],
+ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
+ ]
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK4_BEDTOINTERVALLIST ( input, dict )
- INTERVALLISTTOOLS ( GATK4_BEDTOINTERVALLIST.out.interval_list )
+ GATK4_INTERVALLISTTOOLS ( GATK4_BEDTOINTERVALLIST.out.interval_list )
}
diff --git a/tests/modules/gatk4/intervallisttools/nextflow.config b/tests/modules/gatk4/intervallisttools/nextflow.config
new file mode 100644
index 00000000..b751ad9b
--- /dev/null
+++ b/tests/modules/gatk4/intervallisttools/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_INTERVALLISTTOOLS {
+ ext.args = '--SCATTER_COUNT 6 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --UNIQUE true --SORT true'
+ }
+
+}
diff --git a/tests/modules/gatk4/intervallisttools/test.yml b/tests/modules/gatk4/intervallisttools/test.yml
index da3e6172..c9cb23b8 100644
--- a/tests/modules/gatk4/intervallisttools/test.yml
+++ b/tests/modules/gatk4/intervallisttools/test.yml
@@ -1,16 +1,16 @@
- name: gatk4 intervallisttools test_gatk4_intervallisttools
- command: nextflow run tests/modules/gatk4/intervallisttools -entry test_gatk4_intervallisttools -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/intervallisttools -entry test_gatk4_intervallisttools -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/intervallisttools/nextflow.config
tags:
- gatk4
- gatk4/intervallisttools
files:
- path: output/gatk4/test.interval_list
md5sum: e51101c9357fb2d59fd30e370eefa39c
- - path: output/intervallisttools/test_split/temp_0001_of_6/1scattered.interval_list
+ - path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
md5sum: b8ba8a387200df76a0d1c577626dc265
- - path: output/intervallisttools/test_split/temp_0002_of_6/2scattered.interval_list
+ - path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
md5sum: 0728d164666d9264ef442a493e008dee
- - path: output/intervallisttools/test_split/temp_0003_of_6/3scattered.interval_list
+ - path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
md5sum: 55da0f3c69504148f4e7002a0e072cfe
- - path: output/intervallisttools/test_split/temp_0004_of_6/4scattered.interval_list
+ - path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
md5sum: d29ca4447f32547f2936567fa902796a
diff --git a/tests/modules/gatk4/learnreadorientationmodel/main.nf b/tests/modules/gatk4/learnreadorientationmodel/main.nf
index 1a71873e..dc6e8b89 100644
--- a/tests/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/tests/modules/gatk4/learnreadorientationmodel/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/gatk4/learnreadorientationmodel/main.nf' addParams( options: [suffix:'.artifact-prior'] )
+include { GATK4_LEARNREADORIENTATIONMODEL } from '../../../../modules/gatk4/learnreadorientationmodel/main.nf'
workflow test_gatk4_learnreadorientationmodel {
diff --git a/tests/modules/gatk4/learnreadorientationmodel/nextflow.config b/tests/modules/gatk4/learnreadorientationmodel/nextflow.config
new file mode 100644
index 00000000..3a74623a
--- /dev/null
+++ b/tests/modules/gatk4/learnreadorientationmodel/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_LEARNREADORIENTATIONMODEL {
+ ext.suffix = '.artifact-prior'
+ }
+
+}
diff --git a/tests/modules/gatk4/learnreadorientationmodel/test.yml b/tests/modules/gatk4/learnreadorientationmodel/test.yml
index 6e999fa6..b88df15f 100644
--- a/tests/modules/gatk4/learnreadorientationmodel/test.yml
+++ b/tests/modules/gatk4/learnreadorientationmodel/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 learnreadorientationmodel test_gatk4_learnreadorientationmodel
- command: nextflow run tests/modules/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/learnreadorientationmodel -entry test_gatk4_learnreadorientationmodel -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/learnreadorientationmodel/nextflow.config
tags:
- gatk4
- gatk4/learnreadorientationmodel
diff --git a/tests/modules/gatk4/markduplicates/main.nf b/tests/modules/gatk4/markduplicates/main.nf
index f80c1bd5..90fd866f 100644
--- a/tests/modules/gatk4/markduplicates/main.nf
+++ b/tests/modules/gatk4/markduplicates/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf' addParams( options: [:] )
+include { GATK4_MARKDUPLICATES } from '../../../../modules/gatk4/markduplicates/main.nf'
workflow test_gatk4_markduplicates {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/gatk4/markduplicates/nextflow.config b/tests/modules/gatk4/markduplicates/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/markduplicates/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml
index f4345bc4..0d4c7393 100644
--- a/tests/modules/gatk4/markduplicates/test.yml
+++ b/tests/modules/gatk4/markduplicates/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 markduplicates test_gatk4_markduplicates
- command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
tags:
- gatk4/markduplicates
- gatk4
@@ -11,7 +11,7 @@
- path: output/gatk4/test.metrics
- name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
- command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
tags:
- gatk4/markduplicates
- gatk4
diff --git a/tests/modules/gatk4/mergebamalignment/main.nf b/tests/modules/gatk4/mergebamalignment/main.nf
index 745113ae..59bd833b 100644
--- a/tests/modules/gatk4/mergebamalignment/main.nf
+++ b/tests/modules/gatk4/mergebamalignment/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf' addParams( options: [:] )
+include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf'
workflow test_gatk4_mergebamalignment {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/mergebamalignment/nextflow.config b/tests/modules/gatk4/mergebamalignment/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/mergebamalignment/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/mergebamalignment/test.yml b/tests/modules/gatk4/mergebamalignment/test.yml
index 4fb98e3d..5e1ab8d5 100644
--- a/tests/modules/gatk4/mergebamalignment/test.yml
+++ b/tests/modules/gatk4/mergebamalignment/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 mergebamalignment test_gatk4_mergebamalignment
- command: nextflow run tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config
tags:
- gatk4
- gatk4/mergebamalignment
diff --git a/tests/modules/gatk4/mergevcfs/main.nf b/tests/modules/gatk4/mergevcfs/main.nf
index 5da894ab..fa09d758 100644
--- a/tests/modules/gatk4/mergevcfs/main.nf
+++ b/tests/modules/gatk4/mergevcfs/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_MERGEVCFS } from '../../../../modules/gatk4/mergevcfs/main.nf' addParams( options: [:] )
+include { GATK4_MERGEVCFS } from '../../../../modules/gatk4/mergevcfs/main.nf'
workflow test_gatk4_mergevcfs {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/mergevcfs/nextflow.config b/tests/modules/gatk4/mergevcfs/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/mergevcfs/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/mergevcfs/test.yml b/tests/modules/gatk4/mergevcfs/test.yml
index 884738b0..3ff2bf93 100644
--- a/tests/modules/gatk4/mergevcfs/test.yml
+++ b/tests/modules/gatk4/mergevcfs/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 mergevcfs test_gatk4_mergevcfs
- command: nextflow run tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergevcfs/nextflow.config
tags:
- gatk4/mergevcfs
- gatk4
@@ -8,7 +8,7 @@
md5sum: 5b289bda88d3a3504f2e19ee8cff177c
- name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict
- command: nextflow run tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergevcfs/nextflow.config
tags:
- gatk4/mergevcfs
- gatk4
diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index e163cf9c..f477a0d7 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { GATK4_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf' addParams( options: [:] )
+include { GATK4_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf'
// used to run with the mitochondria mode setting as this increases sensitivity, allowing for some tumor_normal variants to be detected while the old test data is still in use, will be removed when new test data for sarek is available.
-include { GATK4_MUTECT2 as GATK4_TEMPFIX_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf' addParams( options: [args: '--mitochondria-mode'] )
+include { GATK4_MUTECT2 as GATK4_TEMPFIX_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf'
workflow test_gatk4_mutect2_tumor_normal_pair {
input = [ [ id:'test'], // meta map
diff --git a/tests/modules/gatk4/mutect2/nextflow.config b/tests/modules/gatk4/mutect2/nextflow.config
new file mode 100644
index 00000000..0966fc15
--- /dev/null
+++ b/tests/modules/gatk4/mutect2/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_TEMPFIX_MUTECT2 {
+ ext.args = '--mitochondria-mode'
+ }
+
+}
diff --git a/tests/modules/gatk4/mutect2/test.yml b/tests/modules/gatk4/mutect2/test.yml
index 031ed072..c6801e04 100644
--- a/tests/modules/gatk4/mutect2/test.yml
+++ b/tests/modules/gatk4/mutect2/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair
- command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
tags:
- gatk4
- gatk4/mutect2
@@ -11,7 +11,7 @@
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single
- command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
tags:
- gatk4
- gatk4/mutect2
@@ -22,7 +22,7 @@
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_cram_input
- command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_cram_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
tags:
- gatk4
- gatk4/mutect2
@@ -33,7 +33,7 @@
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_generate_pon
- command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_generate_pon -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
tags:
- gatk4
- gatk4/mutect2
@@ -44,7 +44,7 @@
- path: output/gatk4/test.vcf.gz.tbi
- name: gatk4 mutect2 test_gatk4_mutect2_mitochondria
- command: nextflow run tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_mitochondria -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config
tags:
- gatk4
- gatk4/mutect2
diff --git a/tests/modules/gatk4/revertsam/main.nf b/tests/modules/gatk4/revertsam/main.nf
index df127c9b..ab5dddee 100644
--- a/tests/modules/gatk4/revertsam/main.nf
+++ b/tests/modules/gatk4/revertsam/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_REVERTSAM } from '../../../../modules/gatk4/revertsam/main.nf' addParams( options: [:] )
+include { GATK4_REVERTSAM } from '../../../../modules/gatk4/revertsam/main.nf'
workflow test_gatk4_revertsam {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/revertsam/nextflow.config b/tests/modules/gatk4/revertsam/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/revertsam/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/revertsam/test.yml b/tests/modules/gatk4/revertsam/test.yml
index c65d3666..4199b118 100644
--- a/tests/modules/gatk4/revertsam/test.yml
+++ b/tests/modules/gatk4/revertsam/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 revertsam test_gatk4_revertsam
- command: nextflow run tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config
tags:
- gatk4
- gatk4/revertsam
diff --git a/tests/modules/gatk4/samtofastq/main.nf b/tests/modules/gatk4/samtofastq/main.nf
index db63a2a5..26a8ce2d 100644
--- a/tests/modules/gatk4/samtofastq/main.nf
+++ b/tests/modules/gatk4/samtofastq/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_SAMTOFASTQ } from '../../../../modules/gatk4/samtofastq/main.nf' addParams( options: [:] )
+include { GATK4_SAMTOFASTQ } from '../../../../modules/gatk4/samtofastq/main.nf'
workflow test_gatk4_samtofastq_single_end {
input = [ [ id:'test', single_end: true ], // meta map
diff --git a/tests/modules/gatk4/samtofastq/nextflow.config b/tests/modules/gatk4/samtofastq/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/samtofastq/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/samtofastq/test.yml b/tests/modules/gatk4/samtofastq/test.yml
index 3d877d2f..66d3ee4c 100644
--- a/tests/modules/gatk4/samtofastq/test.yml
+++ b/tests/modules/gatk4/samtofastq/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 samtofastq test_gatk4_samtofastq_single_end
- command: nextflow run tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
tags:
- gatk4
- gatk4/samtofastq
@@ -8,7 +8,7 @@
md5sum: 50ace41d4c24467f24f8b929540a7797
- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end
- command: nextflow run tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config
tags:
- gatk4
- gatk4/samtofastq
diff --git a/tests/modules/gatk4/splitncigarreads/main.nf b/tests/modules/gatk4/splitncigarreads/main.nf
index 0934593f..7e5b7c9a 100644
--- a/tests/modules/gatk4/splitncigarreads/main.nf
+++ b/tests/modules/gatk4/splitncigarreads/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarreads/main.nf' addParams( options: [:] )
+include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarreads/main.nf'
workflow test_gatk4_splitncigarreads {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/gatk4/splitncigarreads/nextflow.config b/tests/modules/gatk4/splitncigarreads/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gatk4/splitncigarreads/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml
index 146cd329..1ba8c5cd 100644
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ b/tests/modules/gatk4/splitncigarreads/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads
- command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/splitncigarreads/nextflow.config
tags:
- gatk4
- gatk4/splitncigarreads
diff --git a/tests/modules/gatk4/variantfiltration/main.nf b/tests/modules/gatk4/variantfiltration/main.nf
index 67c9daec..221c469a 100644
--- a/tests/modules/gatk4/variantfiltration/main.nf
+++ b/tests/modules/gatk4/variantfiltration/main.nf
@@ -2,35 +2,38 @@
nextflow.enable.dsl = 2
-test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"', 'suffix': '.filtered']
-include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf' addParams( options: test_options )
+include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf'
// Basic parameters with uncompressed VCF input
workflow test_gatk4_variantfiltration_vcf_input {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true)
+ ]
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+ fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+ fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+ fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
- GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
+ GATK4_VARIANTFILTRATION ( input, fasta, fasta_index, fasta_dict )
}
// Basic parameters with compressed VCF input
workflow test_gatk4_variantfiltration_gz_input {
- input = [ [ id:'test' ], // meta map
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
+ ]
- fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
- fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
- fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+ fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+ fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+ fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
- GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
+ GATK4_VARIANTFILTRATION ( input, fasta, fasta_index, fasta_dict )
}
diff --git a/tests/modules/gatk4/variantfiltration/nextflow.config b/tests/modules/gatk4/variantfiltration/nextflow.config
new file mode 100644
index 00000000..ff2feb9c
--- /dev/null
+++ b/tests/modules/gatk4/variantfiltration/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GATK4_VARIANTFILTRATION {
+ ext.args = "--filter-name \'test_filter\' --filter-expression \'MQ0 > 0\'"
+ ext.suffix = '.filtered'
+ }
+
+}
diff --git a/tests/modules/gatk4/variantfiltration/test.yml b/tests/modules/gatk4/variantfiltration/test.yml
index e3177cfc..b5da0e5c 100644
--- a/tests/modules/gatk4/variantfiltration/test.yml
+++ b/tests/modules/gatk4/variantfiltration/test.yml
@@ -1,5 +1,5 @@
- name: gatk4 variantfiltration test_gatk4_variantfiltration_vcf_input
- command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_vcf_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/variantfiltration/nextflow.config
tags:
- gatk4/variantfiltration
- gatk4
@@ -9,7 +9,7 @@
- path: output/gatk4/test.filtered.vcf.gz.tbi
- name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input
- command: nextflow run tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gatk4/variantfiltration -entry test_gatk4_variantfiltration_gz_input -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/variantfiltration/nextflow.config
tags:
- gatk4/variantfiltration
- gatk4
diff --git a/tests/modules/genmap/index/main.nf b/tests/modules/genmap/index/main.nf
index 358ebb35..06106640 100644
--- a/tests/modules/genmap/index/main.nf
+++ b/tests/modules/genmap/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [publish_dir:'genmap'] )
+include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf'
workflow test_genmap_index {
diff --git a/tests/modules/genmap/index/nextflow.config b/tests/modules/genmap/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/genmap/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/genmap/index/test.yml b/tests/modules/genmap/index/test.yml
index c5078014..ce2098ce 100644
--- a/tests/modules/genmap/index/test.yml
+++ b/tests/modules/genmap/index/test.yml
@@ -1,5 +1,5 @@
- name: genmap index test_genmap_index
- command: nextflow run tests/modules/genmap/index -entry test_genmap_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genmap/index -entry test_genmap_index -c ./tests/config/nextflow.config -c ./tests/modules/genmap/index/nextflow.config
tags:
- genmap
- genmap/index
diff --git a/tests/modules/genmap/mappability/main.nf b/tests/modules/genmap/mappability/main.nf
index 636ec0e4..eb6a34fa 100644
--- a/tests/modules/genmap/mappability/main.nf
+++ b/tests/modules/genmap/mappability/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf' addParams( options: [:] )
-include { GENMAP_MAPPABILITY } from '../../../../modules/genmap/mappability/main.nf' addParams( options: [args : '-K 50 -E 2 -w -t -bg'] )
+include { GENMAP_INDEX } from '../../../../modules/genmap/index/main.nf'
+include { GENMAP_MAPPABILITY } from '../../../../modules/genmap/mappability/main.nf'
workflow test_genmap_map {
diff --git a/tests/modules/genmap/mappability/nextflow.config b/tests/modules/genmap/mappability/nextflow.config
new file mode 100644
index 00000000..6936b9ea
--- /dev/null
+++ b/tests/modules/genmap/mappability/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GENMAP_MAPPABILITY {
+ ext.args = '-K 50 -E 2 -w -t -bg'
+ }
+
+}
diff --git a/tests/modules/genmap/mappability/test.yml b/tests/modules/genmap/mappability/test.yml
index 29a12de1..94c1d501 100644
--- a/tests/modules/genmap/mappability/test.yml
+++ b/tests/modules/genmap/mappability/test.yml
@@ -1,5 +1,5 @@
- name: genmap mappability test_genmap_map
- command: nextflow run tests/modules/genmap/mappability -entry test_genmap_map -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genmap/mappability -entry test_genmap_map -c ./tests/config/nextflow.config -c ./tests/modules/genmap/mappability/nextflow.config
tags:
- genmap
- genmap/mappability
diff --git a/tests/modules/genrich/main.nf b/tests/modules/genrich/main.nf
index aa1a2d49..34db589e 100644
--- a/tests/modules/genrich/main.nf
+++ b/tests/modules/genrich/main.nf
@@ -2,10 +2,10 @@
nextflow.enable.dsl = 2
-include { GENRICH } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.1"] )
-include { GENRICH as GENRICH_CTRL } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.9"] )
-include { GENRICH as GENRICH_ALL } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-r -p 0.1"] )
-include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-j -p 0.1"] )
+include { GENRICH } from '../../../modules/genrich/main.nf'
+include { GENRICH as GENRICH_CTRL } from '../../../modules/genrich/main.nf'
+include { GENRICH as GENRICH_ALL } from '../../../modules/genrich/main.nf'
+include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf'
workflow test_genrich {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/genrich/nextflow.config b/tests/modules/genrich/nextflow.config
new file mode 100644
index 00000000..8f79d7be
--- /dev/null
+++ b/tests/modules/genrich/nextflow.config
@@ -0,0 +1,21 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GENRICH {
+ ext.args = '-p 0.1'
+ }
+
+ withName: GENRICH_CTRL {
+ ext.args = '-p 0.9'
+ }
+
+ withName: GENRICH_ALL {
+ ext.args = '-r -p 0.1'
+ }
+
+ withName: GENRICH_ATACSEQ {
+ ext.args = '-j -p 0.1'
+ }
+
+}
diff --git a/tests/modules/genrich/test.yml b/tests/modules/genrich/test.yml
index 63bf2927..972335c4 100644
--- a/tests/modules/genrich/test.yml
+++ b/tests/modules/genrich/test.yml
@@ -1,5 +1,5 @@
- name: genrich test_genrich
- command: nextflow run tests/modules/genrich -entry test_genrich -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genrich -entry test_genrich -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
tags:
- genrich
files:
@@ -7,7 +7,7 @@
md5sum: 6afabdd3f691c7c84c66ff8a23984681
- name: genrich test_genrich_ctrl
- command: nextflow run tests/modules/genrich -entry test_genrich_ctrl -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genrich -entry test_genrich_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
tags:
- genrich
files:
@@ -15,7 +15,7 @@
md5sum: 2fcc392360b317f5ebee88cdbc149e05
- name: genrich test_genrich_all_outputs
- command: nextflow run tests/modules/genrich -entry test_genrich_all_outputs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genrich -entry test_genrich_all_outputs -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
tags:
- genrich
files:
@@ -31,7 +31,7 @@
md5sum: b14feef34b6d2379a173a734ca963cde
- name: genrich test_genrich_blacklist
- command: nextflow run tests/modules/genrich -entry test_genrich_blacklist -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genrich -entry test_genrich_blacklist -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
tags:
- genrich
files:
@@ -39,7 +39,7 @@
md5sum: 6afabdd3f691c7c84c66ff8a23984681
- name: genrich test_genrich_atacseq
- command: nextflow run tests/modules/genrich -entry test_genrich_atacseq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/genrich -entry test_genrich_atacseq -c ./tests/config/nextflow.config -c ./tests/modules/genrich/nextflow.config
tags:
- genrich
files:
diff --git a/tests/modules/gffread/main.nf b/tests/modules/gffread/main.nf
index 87e95275..6ab7922b 100644
--- a/tests/modules/gffread/main.nf
+++ b/tests/modules/gffread/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GFFREAD } from '../../../modules/gffread/main.nf' addParams( options: [suffix: '.out'] )
+include { GFFREAD } from '../../../modules/gffread/main.nf'
workflow test_gffread {
input = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
diff --git a/tests/modules/gffread/nextflow.config b/tests/modules/gffread/nextflow.config
new file mode 100644
index 00000000..00c052f5
--- /dev/null
+++ b/tests/modules/gffread/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GFFREAD {
+ ext.suffix = '.out'
+ }
+
+}
diff --git a/tests/modules/gffread/test.yml b/tests/modules/gffread/test.yml
index 48096f1e..c5a16132 100644
--- a/tests/modules/gffread/test.yml
+++ b/tests/modules/gffread/test.yml
@@ -1,5 +1,5 @@
- name: gffread
- command: nextflow run ./tests/modules/gffread/ -entry test_gffread -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gffread/ -entry test_gffread -c ./tests/config/nextflow.config -c ./tests/modules/gffread/nextflow.config
tags:
- gffread
files:
diff --git a/tests/modules/glnexus/main.nf b/tests/modules/glnexus/main.nf
index 2a79b2fa..aeb7c7e2 100644
--- a/tests/modules/glnexus/main.nf
+++ b/tests/modules/glnexus/main.nf
@@ -2,12 +2,16 @@
nextflow.enable.dsl = 2
-include { GLNEXUS } from '../../../modules/glnexus/main.nf' addParams( options: [:] )
+include { GLNEXUS } from '../../../modules/glnexus/main.nf'
workflow test_glnexus {
- input = [ [ id:'test' ], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test' ], // meta map
+ [
+ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true)
+ ]
+ ]
+
GLNEXUS ( input )
}
diff --git a/tests/modules/glnexus/nextflow.config b/tests/modules/glnexus/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/glnexus/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/glnexus/test.yml b/tests/modules/glnexus/test.yml
index c7b255ee..bfca4529 100644
--- a/tests/modules/glnexus/test.yml
+++ b/tests/modules/glnexus/test.yml
@@ -1,7 +1,7 @@
- name: glnexus test_glnexus
- command: nextflow run tests/modules/glnexus -entry test_glnexus -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/glnexus -entry test_glnexus -c ./tests/config/nextflow.config -c ./tests/modules/glnexus/nextflow.config
tags:
- glnexus
files:
- path: output/glnexus/test.bcf
- md5sum: 33ac8c9f3ff54e6a23177ba94a449173
+ md5sum: 62b2cea9c1b92ac63645cb031eea46fc
diff --git a/tests/modules/graphmap2/align/main.nf b/tests/modules/graphmap2/align/main.nf
index 0cd885ab..96b95166 100644
--- a/tests/modules/graphmap2/align/main.nf
+++ b/tests/modules/graphmap2/align/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf' addParams( options: [:] )
-include { GRAPHMAP2_ALIGN } from '../../../../modules/graphmap2/align/main.nf' addParams( options: [:] )
+include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf'
+include { GRAPHMAP2_ALIGN } from '../../../../modules/graphmap2/align/main.nf'
workflow test_graphmap2_align {
diff --git a/tests/modules/graphmap2/align/nextflow.config b/tests/modules/graphmap2/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/graphmap2/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/graphmap2/align/test.yml b/tests/modules/graphmap2/align/test.yml
index 7e90b8d4..90e52dd1 100644
--- a/tests/modules/graphmap2/align/test.yml
+++ b/tests/modules/graphmap2/align/test.yml
@@ -1,5 +1,5 @@
- name: graphmap2 align
- command: nextflow run ./tests/modules/graphmap2/align -entry test_graphmap2_align -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/graphmap2/align -entry test_graphmap2_align -c ./tests/config/nextflow.config -c ./tests/modules/graphmap2/align/nextflow.config
tags:
- graphmap2
- graphmap2/align
diff --git a/tests/modules/graphmap2/index/main.nf b/tests/modules/graphmap2/index/main.nf
index 66347f06..3c449c6b 100644
--- a/tests/modules/graphmap2/index/main.nf
+++ b/tests/modules/graphmap2/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf' addParams( options: [:] )
+include { GRAPHMAP2_INDEX } from '../../../../modules/graphmap2/index/main.nf'
workflow test_graphmap2_index {
diff --git a/tests/modules/graphmap2/index/nextflow.config b/tests/modules/graphmap2/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/graphmap2/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/graphmap2/index/test.yml b/tests/modules/graphmap2/index/test.yml
index 15042e97..0bff487e 100644
--- a/tests/modules/graphmap2/index/test.yml
+++ b/tests/modules/graphmap2/index/test.yml
@@ -1,5 +1,5 @@
- name: graphmap2 index
- command: nextflow run ./tests/modules/graphmap2/index -entry test_graphmap2_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/graphmap2/index -entry test_graphmap2_index -c ./tests/config/nextflow.config -c ./tests/modules/graphmap2/index/nextflow.config
tags:
- graphmap2
- graphmap2/index
diff --git a/tests/modules/gstama/collapse/main.nf b/tests/modules/gstama/collapse/main.nf
index 70b3c741..3eb97767 100644
--- a/tests/modules/gstama/collapse/main.nf
+++ b/tests/modules/gstama/collapse/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GSTAMA_COLLAPSE } from '../../../../modules/gstama/collapse/main.nf' addParams( options: [ args:"-x capped -b BAM", suffix:'_tc' ] )
+include { GSTAMA_COLLAPSE } from '../../../../modules/gstama/collapse/main.nf'
workflow test_gstama_collapse {
diff --git a/tests/modules/gstama/collapse/nextflow.config b/tests/modules/gstama/collapse/nextflow.config
new file mode 100644
index 00000000..0455c8b2
--- /dev/null
+++ b/tests/modules/gstama/collapse/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GSTAMA_COLLAPSE {
+ ext.args = '-x capped -b BAM'
+ ext.suffix = '_tc'
+ }
+
+}
diff --git a/tests/modules/gstama/collapse/test.yml b/tests/modules/gstama/collapse/test.yml
index 3815a156..50d3775e 100644
--- a/tests/modules/gstama/collapse/test.yml
+++ b/tests/modules/gstama/collapse/test.yml
@@ -1,5 +1,5 @@
- name: gstama collapse test_gstama_collapse
- command: nextflow run tests/modules/gstama/collapse -entry test_gstama_collapse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gstama/collapse -entry test_gstama_collapse -c ./tests/config/nextflow.config -c ./tests/modules/gstama/collapse/nextflow.config
tags:
- gstama
- gstama/collapse
diff --git a/tests/modules/gstama/merge/main.nf b/tests/modules/gstama/merge/main.nf
index f9a8e05f..4a9102a2 100644
--- a/tests/modules/gstama/merge/main.nf
+++ b/tests/modules/gstama/merge/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GSTAMA_MERGE } from '../../../../modules/gstama/merge/main' addParams( options: [suffix:'_merged'] )
+include { GSTAMA_MERGE } from '../../../../modules/gstama/merge/main'
workflow test_gstama_merge {
diff --git a/tests/modules/gstama/merge/nextflow.config b/tests/modules/gstama/merge/nextflow.config
new file mode 100644
index 00000000..a9c63fcf
--- /dev/null
+++ b/tests/modules/gstama/merge/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GSTAMA_MERGE {
+ ext.suffix = '_merged'
+ }
+
+}
diff --git a/tests/modules/gstama/merge/test.yml b/tests/modules/gstama/merge/test.yml
index b98e35b6..1db35d15 100644
--- a/tests/modules/gstama/merge/test.yml
+++ b/tests/modules/gstama/merge/test.yml
@@ -1,5 +1,5 @@
- name: gstama merge test_gstama_merge
- command: nextflow run tests/modules/gstama/merge -entry test_gstama_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gstama/merge -entry test_gstama_merge -c ./tests/config/nextflow.config -c ./tests/modules/gstama/merge/nextflow.config
tags:
- gstama
- gstama/merge
diff --git a/tests/modules/gtdbtk/classifywf/main.nf b/tests/modules/gtdbtk/classifywf/main.nf
index f52b0ccc..1517d7cc 100644
--- a/tests/modules/gtdbtk/classifywf/main.nf
+++ b/tests/modules/gtdbtk/classifywf/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GTDBTK_CLASSIFYWF } from '../../../../modules/gtdbtk/classifywf/main.nf' addParams( options: [:] )
+include { GTDBTK_CLASSIFYWF } from '../../../../modules/gtdbtk/classifywf/main.nf'
process STUB_GTDBTK_DATABASE {
output:
diff --git a/tests/modules/gtdbtk/classifywf/nextflow.config b/tests/modules/gtdbtk/classifywf/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gtdbtk/classifywf/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gtdbtk/classifywf/test.yml b/tests/modules/gtdbtk/classifywf/test.yml
index 6d0f055e..e24f1e17 100644
--- a/tests/modules/gtdbtk/classifywf/test.yml
+++ b/tests/modules/gtdbtk/classifywf/test.yml
@@ -1,5 +1,5 @@
- name: gtdbtk classifywf
- command: nextflow run ./tests/modules/gtdbtk/classifywf -entry test_gtdbtk_classifywf -c tests/config/nextflow.config -stub-run
+ command: nextflow run ./tests/modules/gtdbtk/classifywf -entry test_gtdbtk_classifywf -c ./tests/config/nextflow.config -stub-run -c ./tests/modules/gtdbtk/classifywf/nextflow.config
tags:
- gtdbtk
- gtdbtk/classifywf
diff --git a/tests/modules/gubbins/main.nf b/tests/modules/gubbins/main.nf
index 87e164d0..342150b3 100644
--- a/tests/modules/gubbins/main.nf
+++ b/tests/modules/gubbins/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GUBBINS } from '../../../modules/gubbins/main.nf' addParams( options: [:] )
+include { GUBBINS } from '../../../modules/gubbins/main.nf'
workflow test_gubbins {
input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true)
diff --git a/tests/modules/gubbins/nextflow.config b/tests/modules/gubbins/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gubbins/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gubbins/test.yml b/tests/modules/gubbins/test.yml
index 7bc0216b..6c85260d 100644
--- a/tests/modules/gubbins/test.yml
+++ b/tests/modules/gubbins/test.yml
@@ -1,5 +1,5 @@
- name: gubbins
- command: nextflow run ./tests/modules/gubbins -entry test_gubbins -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gubbins -entry test_gubbins -c ./tests/config/nextflow.config -c ./tests/modules/gubbins/nextflow.config
tags:
- gubbins
files:
diff --git a/tests/modules/gunc/downloaddb/main.nf b/tests/modules/gunc/downloaddb/main.nf
index c0321279..3e3126f5 100644
--- a/tests/modules/gunc/downloaddb/main.nf
+++ b/tests/modules/gunc/downloaddb/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf' addParams( options: [:] )
+include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf'
workflow test_gunc_downloaddb {
diff --git a/tests/modules/gunc/downloaddb/nextflow.config b/tests/modules/gunc/downloaddb/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gunc/downloaddb/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gunc/downloaddb/test.yml b/tests/modules/gunc/downloaddb/test.yml
index d1aafae7..4e1c23f8 100644
--- a/tests/modules/gunc/downloaddb/test.yml
+++ b/tests/modules/gunc/downloaddb/test.yml
@@ -1,5 +1,5 @@
- name: gunc downloaddb
- command: nextflow run ./tests/modules/gunc/downloaddb -entry test_gunc_downloaddb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gunc/downloaddb -entry test_gunc_downloaddb -c ./tests/config/nextflow.config -c ./tests/modules/gunc/downloaddb/nextflow.config
tags:
- gunc
- gunc/downloaddb
diff --git a/tests/modules/gunc/run/main.nf b/tests/modules/gunc/run/main.nf
index a1a191dc..28ecd35f 100644
--- a/tests/modules/gunc/run/main.nf
+++ b/tests/modules/gunc/run/main.nf
@@ -2,16 +2,16 @@
nextflow.enable.dsl = 2
-include { GUNC_RUN } from '../../../../modules/gunc/run/main.nf' addParams( options: [:] )
-include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf' addParams( options: [:] )
-
+include { GUNC_RUN } from '../../../../modules/gunc/run/main.nf'
+include { GUNC_DOWNLOADDB } from '../../../../modules/gunc/downloaddb/main.nf'
workflow test_gunc_run {
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
-
- GUNC_DOWNLOADDB('progenomes')
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+ ]
+ GUNC_DOWNLOADDB ( 'progenomes' )
GUNC_RUN ( input, GUNC_DOWNLOADDB.out.db )
}
diff --git a/tests/modules/gunc/run/nextflow.config b/tests/modules/gunc/run/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gunc/run/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gunc/run/test.yml b/tests/modules/gunc/run/test.yml
index d527f37e..5bcef868 100644
--- a/tests/modules/gunc/run/test.yml
+++ b/tests/modules/gunc/run/test.yml
@@ -1,5 +1,5 @@
- name: gunc run
- command: nextflow run ./tests/modules/gunc/run -entry test_gunc_run -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gunc/run -entry test_gunc_run -c ./tests/config/nextflow.config -c ./tests/modules/gunc/run/nextflow.config
tags:
- gunc
- gunc/run
diff --git a/tests/modules/gunzip/main.nf b/tests/modules/gunzip/main.nf
index 0c23a8cd..3d41a4a2 100644
--- a/tests/modules/gunzip/main.nf
+++ b/tests/modules/gunzip/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { GUNZIP } from '../../../modules/gunzip/main.nf' addParams( options: [:] )
+include { GUNZIP } from '../../../modules/gunzip/main.nf'
workflow test_gunzip {
input = [ [],
diff --git a/tests/modules/gunzip/nextflow.config b/tests/modules/gunzip/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/gunzip/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/gunzip/test.yml b/tests/modules/gunzip/test.yml
index 70012b21..70e95d6b 100644
--- a/tests/modules/gunzip/test.yml
+++ b/tests/modules/gunzip/test.yml
@@ -1,5 +1,5 @@
- name: gunzip
- command: nextflow run ./tests/modules/gunzip -entry test_gunzip -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/gunzip -entry test_gunzip -c ./tests/config/nextflow.config -c ./tests/modules/gunzip/nextflow.config
tags:
- gunzip
files:
diff --git a/tests/modules/hicap/main.nf b/tests/modules/hicap/main.nf
index 3ac9c20b..82c515de 100644
--- a/tests/modules/hicap/main.nf
+++ b/tests/modules/hicap/main.nf
@@ -2,13 +2,14 @@
nextflow.enable.dsl = 2
-include { HICAP } from '../../../modules/hicap/main.nf' addParams( options: [:] )
+include { HICAP } from '../../../modules/hicap/main.nf'
workflow test_hicap {
-
- input = [ [ id:'test', single_end:false ], // meta map
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/species/haemophilus_influenzae/genome/GCF_900478275.fna.gz", checkIfExists: true) ]
-
+
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+ ]
database_dir = []
model_fp = []
diff --git a/tests/modules/hicap/nextflow.config b/tests/modules/hicap/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hicap/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hicap/test.yml b/tests/modules/hicap/test.yml
index 8c8420fd..0cce28c7 100644
--- a/tests/modules/hicap/test.yml
+++ b/tests/modules/hicap/test.yml
@@ -1,10 +1,10 @@
- name: hicap test_hicap
- command: nextflow run tests/modules/hicap -entry test_hicap -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hicap -entry test_hicap -c ./tests/config/nextflow.config -c ./tests/modules/hicap/nextflow.config
tags:
- hicap
files:
- - path: output/hicap/GCF_900478275.gbk
+ - path: output/hicap/genome.gbk
md5sum: 562d026956903354ac80721f501335d4
- - path: output/hicap/GCF_900478275.svg
+ - path: output/hicap/genome.svg
md5sum: 4fb94871dd0fdd8b4496049668176631
- - path: output/hicap/GCF_900478275.tsv
+ - path: output/hicap/genome.tsv
diff --git a/tests/modules/hifiasm/main.nf b/tests/modules/hifiasm/main.nf
index 30614389..f0e2a0f4 100644
--- a/tests/modules/hifiasm/main.nf
+++ b/tests/modules/hifiasm/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HIFIASM } from '../../../modules/hifiasm/main.nf' addParams( options: [args:'-f0'] )
+include { HIFIASM } from '../../../modules/hifiasm/main.nf'
/*
* Test with long reads only
diff --git a/tests/modules/hifiasm/nextflow.config b/tests/modules/hifiasm/nextflow.config
new file mode 100644
index 00000000..0994c901
--- /dev/null
+++ b/tests/modules/hifiasm/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: HIFIASM {
+ ext.args = '-f0'
+ }
+
+}
diff --git a/tests/modules/hifiasm/test.yml b/tests/modules/hifiasm/test.yml
index 47d9e38f..f7e3e6ae 100644
--- a/tests/modules/hifiasm/test.yml
+++ b/tests/modules/hifiasm/test.yml
@@ -1,5 +1,5 @@
- name: hifiasm test_hifiasm_hifi_only
- command: nextflow run tests/modules/hifiasm -entry test_hifiasm_hifi_only -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hifiasm -entry test_hifiasm_hifi_only -c ./tests/config/nextflow.config -c ./tests/modules/hifiasm/nextflow.config
tags:
- hifiasm
files:
@@ -16,7 +16,7 @@
- path: output/hifiasm/test.asm.ovlp.source.bin
- name: hifiasm test_hifiasm_with_parental_reads
- command: nextflow run tests/modules/hifiasm -entry test_hifiasm_with_parental_reads -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hifiasm -entry test_hifiasm_with_parental_reads -c ./tests/config/nextflow.config -c ./tests/modules/hifiasm/nextflow.config
tags:
- hifiasm
files:
diff --git a/tests/modules/hisat2/align/main.nf b/tests/modules/hisat2/align/main.nf
index 7bbe3a4b..17b47c93 100644
--- a/tests/modules/hisat2/align/main.nf
+++ b/tests/modules/hisat2/align/main.nf
@@ -2,14 +2,17 @@
nextflow.enable.dsl = 2
-include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' addParams( options: [:] )
-include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf' addParams( options: [:] )
-include { HISAT2_ALIGN } from '../../../../modules/hisat2/align/main.nf' addParams( options: [:] )
+include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf'
+include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf'
+include { HISAT2_ALIGN } from '../../../../modules/hisat2/align/main.nf'
workflow test_hisat2_align_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
@@ -19,10 +22,13 @@ workflow test_hisat2_align_single_end {
}
workflow test_hisat2_align_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
diff --git a/tests/modules/hisat2/align/nextflow.config b/tests/modules/hisat2/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hisat2/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hisat2/align/test.yml b/tests/modules/hisat2/align/test.yml
index 1c6c8ac2..54e263bc 100644
--- a/tests/modules/hisat2/align/test.yml
+++ b/tests/modules/hisat2/align/test.yml
@@ -1,5 +1,5 @@
- name: hisat2 align test_hisat2_align_single_end
- command: nextflow run tests/modules/hisat2/align -entry test_hisat2_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hisat2/align -entry test_hisat2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/align/nextflow.config
tags:
- hisat2
- hisat2/align
@@ -9,25 +9,25 @@
- path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/hisat2/test.bam
- - path: output/index/hisat2/genome.5.ht2
+ - path: output/hisat2/hisat2/genome.5.ht2
md5sum: 91198831aaba993acac1734138c5f173
- - path: output/index/hisat2/genome.7.ht2
+ - path: output/hisat2/hisat2/genome.7.ht2
md5sum: 9013eccd91ad614d7893c739275a394f
- - path: output/index/hisat2/genome.1.ht2
+ - path: output/hisat2/hisat2/genome.1.ht2
md5sum: 057cfa8a22b97ee9cff4c8d342498803
- - path: output/index/hisat2/genome.2.ht2
+ - path: output/hisat2/hisat2/genome.2.ht2
md5sum: 47b153cd1319abc88dda532462651fcf
- - path: output/index/hisat2/genome.6.ht2
+ - path: output/hisat2/hisat2/genome.6.ht2
md5sum: 265e1284ce85686516fae5d35540994a
- - path: output/index/hisat2/genome.3.ht2
+ - path: output/hisat2/hisat2/genome.3.ht2
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: output/index/hisat2/genome.8.ht2
+ - path: output/hisat2/hisat2/genome.8.ht2
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- - path: output/index/hisat2/genome.4.ht2
+ - path: output/hisat2/hisat2/genome.4.ht2
md5sum: c25be5f8b0378abf7a58c8a880b87626
- name: hisat2 align test_hisat2_align_paired_end
- command: nextflow run tests/modules/hisat2/align -entry test_hisat2_align_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hisat2/align -entry test_hisat2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/align/nextflow.config
tags:
- hisat2
- hisat2/align
@@ -37,19 +37,19 @@
- path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/hisat2/test.bam
- - path: output/index/hisat2/genome.5.ht2
+ - path: output/hisat2/hisat2/genome.5.ht2
md5sum: 91198831aaba993acac1734138c5f173
- - path: output/index/hisat2/genome.7.ht2
+ - path: output/hisat2/hisat2/genome.7.ht2
md5sum: 9013eccd91ad614d7893c739275a394f
- - path: output/index/hisat2/genome.1.ht2
+ - path: output/hisat2/hisat2/genome.1.ht2
md5sum: 057cfa8a22b97ee9cff4c8d342498803
- - path: output/index/hisat2/genome.2.ht2
+ - path: output/hisat2/hisat2/genome.2.ht2
md5sum: 47b153cd1319abc88dda532462651fcf
- - path: output/index/hisat2/genome.6.ht2
+ - path: output/hisat2/hisat2/genome.6.ht2
md5sum: 265e1284ce85686516fae5d35540994a
- - path: output/index/hisat2/genome.3.ht2
+ - path: output/hisat2/hisat2/genome.3.ht2
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: output/index/hisat2/genome.8.ht2
+ - path: output/hisat2/hisat2/genome.8.ht2
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- - path: output/index/hisat2/genome.4.ht2
+ - path: output/hisat2/hisat2/genome.4.ht2
md5sum: c25be5f8b0378abf7a58c8a880b87626
diff --git a/tests/modules/hisat2/build_test/main.nf b/tests/modules/hisat2/build_test/main.nf
index f40f47cc..a0c14dc8 100644
--- a/tests/modules/hisat2/build_test/main.nf
+++ b/tests/modules/hisat2/build_test/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' addParams( options: [:] )
-include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf' addParams( options: [:] )
+include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf'
+include { HISAT2_BUILD } from '../../../../modules/hisat2/build/main.nf'
workflow test_hisat2_build {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/hisat2/build_test/nextflow.config b/tests/modules/hisat2/build_test/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hisat2/build_test/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hisat2/build_test/test.yml b/tests/modules/hisat2/build_test/test.yml
index a8bb2390..da5a450c 100644
--- a/tests/modules/hisat2/build_test/test.yml
+++ b/tests/modules/hisat2/build_test/test.yml
@@ -1,24 +1,24 @@
- name: hisat2 build test_hisat2_build
- command: nextflow run tests/modules/hisat2/build_test -entry test_hisat2_build -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hisat2/build_test -entry test_hisat2_build -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/build/nextflow.config
tags:
- hisat2
- hisat2/build
files:
- path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- - path: output/index/hisat2/genome.5.ht2
+ - path: output/hisat2/hisat2/genome.5.ht2
md5sum: 91198831aaba993acac1734138c5f173
- - path: output/index/hisat2/genome.7.ht2
+ - path: output/hisat2/hisat2/genome.7.ht2
md5sum: 9013eccd91ad614d7893c739275a394f
- - path: output/index/hisat2/genome.1.ht2
+ - path: output/hisat2/hisat2/genome.1.ht2
md5sum: 057cfa8a22b97ee9cff4c8d342498803
- - path: output/index/hisat2/genome.2.ht2
+ - path: output/hisat2/hisat2/genome.2.ht2
md5sum: 47b153cd1319abc88dda532462651fcf
- - path: output/index/hisat2/genome.6.ht2
+ - path: output/hisat2/hisat2/genome.6.ht2
md5sum: 265e1284ce85686516fae5d35540994a
- - path: output/index/hisat2/genome.3.ht2
+ - path: output/hisat2/hisat2/genome.3.ht2
md5sum: 4ed93abba181d8dfab2e303e33114777
- - path: output/index/hisat2/genome.8.ht2
+ - path: output/hisat2/hisat2/genome.8.ht2
md5sum: 33cdeccccebe80329f1fdbee7f5874cb
- - path: output/index/hisat2/genome.4.ht2
+ - path: output/hisat2/hisat2/genome.4.ht2
md5sum: c25be5f8b0378abf7a58c8a880b87626
diff --git a/tests/modules/hisat2/extractsplicesites/main.nf b/tests/modules/hisat2/extractsplicesites/main.nf
index 5c7e17b9..e947717e 100644
--- a/tests/modules/hisat2/extractsplicesites/main.nf
+++ b/tests/modules/hisat2/extractsplicesites/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf' addParams( options: [:] )
+include { HISAT2_EXTRACTSPLICESITES } from '../../../../modules/hisat2/extractsplicesites/main.nf'
workflow test_hisat2_extractsplicesites {
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
diff --git a/tests/modules/hisat2/extractsplicesites/nextflow.config b/tests/modules/hisat2/extractsplicesites/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hisat2/extractsplicesites/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hisat2/extractsplicesites/test.yml b/tests/modules/hisat2/extractsplicesites/test.yml
index a3e29346..a528199c 100644
--- a/tests/modules/hisat2/extractsplicesites/test.yml
+++ b/tests/modules/hisat2/extractsplicesites/test.yml
@@ -1,5 +1,5 @@
- name: hisat2 extractsplicesites test_hisat2_extractsplicesites
- command: nextflow run tests/modules/hisat2/extractsplicesites -entry test_hisat2_extractsplicesites -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hisat2/extractsplicesites -entry test_hisat2_extractsplicesites -c ./tests/config/nextflow.config -c ./tests/modules/hisat2/extractsplicesites/nextflow.config
tags:
- hisat2
- hisat2/extractsplicesites
diff --git a/tests/modules/hmmcopy/gccounter/main.nf b/tests/modules/hmmcopy/gccounter/main.nf
index 30846ca9..05728bf5 100644
--- a/tests/modules/hmmcopy/gccounter/main.nf
+++ b/tests/modules/hmmcopy/gccounter/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf' addParams( options: [:] )
+include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf'
workflow test_hmmcopy_gccounter {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/hmmcopy/gccounter/nextflow.config b/tests/modules/hmmcopy/gccounter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hmmcopy/gccounter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hmmcopy/gccounter/test.yml b/tests/modules/hmmcopy/gccounter/test.yml
index edcd6b92..1cd20273 100644
--- a/tests/modules/hmmcopy/gccounter/test.yml
+++ b/tests/modules/hmmcopy/gccounter/test.yml
@@ -1,5 +1,5 @@
- name: hmmcopy gccounter test_hmmcopy_gccounter
- command: nextflow run tests/modules/hmmcopy/gccounter -entry test_hmmcopy_gccounter -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hmmcopy/gccounter -entry test_hmmcopy_gccounter -c ./tests/config/nextflow.config -c ./tests/modules/hmmcopy/gccounter/nextflow.config
tags:
- hmmcopy
- hmmcopy/gccounter
diff --git a/tests/modules/hmmcopy/readcounter/main.nf b/tests/modules/hmmcopy/readcounter/main.nf
index 9025f98e..21737aab 100644
--- a/tests/modules/hmmcopy/readcounter/main.nf
+++ b/tests/modules/hmmcopy/readcounter/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf' addParams( options: [:] )
+include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf'
workflow test_hmmcopy_readcounter {
diff --git a/tests/modules/hmmcopy/readcounter/nextflow.config b/tests/modules/hmmcopy/readcounter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hmmcopy/readcounter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hmmcopy/readcounter/test.yml b/tests/modules/hmmcopy/readcounter/test.yml
index 6c00ee08..a7e84f35 100644
--- a/tests/modules/hmmcopy/readcounter/test.yml
+++ b/tests/modules/hmmcopy/readcounter/test.yml
@@ -1,5 +1,5 @@
- name: hmmcopy readcounter test_hmmcopy_readcounter
- command: nextflow run tests/modules/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c ./tests/config/nextflow.config -c ./tests/modules/hmmcopy/readcounter/nextflow.config
tags:
- hmmcopy
- hmmcopy/readcounter
diff --git a/tests/modules/hmmer/hmmalign/main.nf b/tests/modules/hmmer/hmmalign/main.nf
index 55194dc6..3bf6d452 100644
--- a/tests/modules/hmmer/hmmalign/main.nf
+++ b/tests/modules/hmmer/hmmalign/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HMMER_HMMALIGN } from '../../../../modules/hmmer/hmmalign/main.nf' addParams( options: [:] )
+include { HMMER_HMMALIGN } from '../../../../modules/hmmer/hmmalign/main.nf'
workflow test_hmmer_hmmalign {
diff --git a/tests/modules/hmmer/hmmalign/nextflow.config b/tests/modules/hmmer/hmmalign/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/hmmer/hmmalign/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/hmmer/hmmalign/test.yml b/tests/modules/hmmer/hmmalign/test.yml
index 4afb34ca..2e5ccfaf 100644
--- a/tests/modules/hmmer/hmmalign/test.yml
+++ b/tests/modules/hmmer/hmmalign/test.yml
@@ -1,5 +1,5 @@
- name: hmmer hmmalign test_hmmer_hmmalign
- command: nextflow run tests/modules/hmmer/hmmalign -entry test_hmmer_hmmalign -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/hmmer/hmmalign -entry test_hmmer_hmmalign -c ./tests/config/nextflow.config -c ./tests/modules/hmmer/hmmalign/nextflow.config
tags:
- hmmer
- hmmer/hmmalign
diff --git a/tests/modules/homer/annotatepeaks/main.nf b/tests/modules/homer/annotatepeaks/main.nf
index b146c857..ab8f6f8f 100644
--- a/tests/modules/homer/annotatepeaks/main.nf
+++ b/tests/modules/homer/annotatepeaks/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HOMER_ANNOTATEPEAKS } from '../../../../modules/homer/annotatepeaks/main.nf' addParams( options: [:] )
+include { HOMER_ANNOTATEPEAKS } from '../../../../modules/homer/annotatepeaks/main.nf'
workflow test_homer_annotatepeaks {
input = [ [ id:'test'],
diff --git a/tests/modules/homer/annotatepeaks/nextflow.config b/tests/modules/homer/annotatepeaks/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/homer/annotatepeaks/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/homer/annotatepeaks/test.yml b/tests/modules/homer/annotatepeaks/test.yml
index fed0f82e..52fd99a3 100644
--- a/tests/modules/homer/annotatepeaks/test.yml
+++ b/tests/modules/homer/annotatepeaks/test.yml
@@ -1,5 +1,5 @@
- name: homer annotatepeaks test_homer_annotatepeaks
- command: nextflow run tests/modules/homer/annotatepeaks -entry test_homer_annotatepeaks -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/homer/annotatepeaks -entry test_homer_annotatepeaks -c ./tests/config/nextflow.config -c ./tests/modules/homer/annotatepeaks/nextflow.config
tags:
- homer
- homer/annotatepeaks
diff --git a/tests/modules/homer/findpeaks/main.nf b/tests/modules/homer/findpeaks/main.nf
index 06d44bdf..0e7e8ed6 100644
--- a/tests/modules/homer/findpeaks/main.nf
+++ b/tests/modules/homer/findpeaks/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' addParams( options: [args: '-format bed'] )
-include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf' addParams( options: [args: '-style factor'] )
+include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
+include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf'
workflow test_homer_findpeaks {
input = [[id:'test'],
diff --git a/tests/modules/homer/findpeaks/nextflow.config b/tests/modules/homer/findpeaks/nextflow.config
new file mode 100644
index 00000000..9a921a3c
--- /dev/null
+++ b/tests/modules/homer/findpeaks/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: HOMER_MAKETAGDIRECTORY {
+ ext.args = '-format bed'
+ }
+
+ withName: HOMER_FINDPEAKS {
+ ext.args = '-style factor'
+ }
+
+}
diff --git a/tests/modules/homer/findpeaks/test.yml b/tests/modules/homer/findpeaks/test.yml
index b0b1a0df..75e94529 100644
--- a/tests/modules/homer/findpeaks/test.yml
+++ b/tests/modules/homer/findpeaks/test.yml
@@ -1,5 +1,5 @@
- name: homer findpeaks
- command: nextflow run ./tests/modules/homer/findpeaks -entry test_homer_findpeaks -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/homer/findpeaks -entry test_homer_findpeaks -c ./tests/config/nextflow.config -c ./tests/modules/homer/findpeaks/nextflow.config
tags:
- homer
- homer/findpeaks
diff --git a/tests/modules/homer/maketagdirectory/main.nf b/tests/modules/homer/maketagdirectory/main.nf
index 897aac1f..766aff0d 100644
--- a/tests/modules/homer/maketagdirectory/main.nf
+++ b/tests/modules/homer/maketagdirectory/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' addParams( options: [args: '-format bed'] )
+include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
workflow test_homer_maketagdirectory {
input = [[id:'test'],
diff --git a/tests/modules/homer/maketagdirectory/nextflow.config b/tests/modules/homer/maketagdirectory/nextflow.config
new file mode 100644
index 00000000..81587d69
--- /dev/null
+++ b/tests/modules/homer/maketagdirectory/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: HOMER_MAKETAGDIRECTORY {
+ ext.args = '-format bed'
+ }
+
+}
diff --git a/tests/modules/homer/maketagdirectory/test.yml b/tests/modules/homer/maketagdirectory/test.yml
index 80112c0b..746c6ef6 100644
--- a/tests/modules/homer/maketagdirectory/test.yml
+++ b/tests/modules/homer/maketagdirectory/test.yml
@@ -1,5 +1,5 @@
- name: homer maketagdirectory
- command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
tags:
- homer
- homer/maketagdirectory
@@ -16,7 +16,7 @@
md5sum: e5aa2b9843ca9c04ace297280aed6af4
- name: homer meta maketagdirectory
- command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_meta_maketagdirectory -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_meta_maketagdirectory -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
tags:
- homer
- homer/maketagdirectory
diff --git a/tests/modules/homer/makeucscfile/main.nf b/tests/modules/homer/makeucscfile/main.nf
index 5ed75959..986c9c14 100644
--- a/tests/modules/homer/makeucscfile/main.nf
+++ b/tests/modules/homer/makeucscfile/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf' addParams( options: [args: '-format bed'] )
-include { HOMER_MAKEUCSCFILE } from '../../../../modules/homer/makeucscfile/main.nf' addParams( options: [:] )
+include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
+include { HOMER_MAKEUCSCFILE } from '../../../../modules/homer/makeucscfile/main.nf'
workflow test_homer_makeucscfile {
input = [[id:'test'],
diff --git a/tests/modules/homer/makeucscfile/nextflow.config b/tests/modules/homer/makeucscfile/nextflow.config
new file mode 100644
index 00000000..81587d69
--- /dev/null
+++ b/tests/modules/homer/makeucscfile/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: HOMER_MAKETAGDIRECTORY {
+ ext.args = '-format bed'
+ }
+
+}
diff --git a/tests/modules/homer/makeucscfile/test.yml b/tests/modules/homer/makeucscfile/test.yml
index 4d337f41..cf3d1b4d 100644
--- a/tests/modules/homer/makeucscfile/test.yml
+++ b/tests/modules/homer/makeucscfile/test.yml
@@ -1,5 +1,5 @@
- name: homer makeucscfile
- command: nextflow run ./tests/modules/homer/makeucscfile -entry test_homer_makeucscfile -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/homer/makeucscfile -entry test_homer_makeucscfile -c ./tests/config/nextflow.config -c ./tests/modules/homer/makeucscfile/nextflow.config
tags:
- homer
- homer/makeucscfile
diff --git a/tests/modules/idr/main.nf b/tests/modules/idr/main.nf
index aa141a57..ed3bf289 100644
--- a/tests/modules/idr/main.nf
+++ b/tests/modules/idr/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { IDR } from '../../../modules/idr/main.nf' addParams( options: [:] )
+include { IDR } from '../../../modules/idr/main.nf'
workflow test_idr_narrowpeak {
diff --git a/tests/modules/idr/nextflow.config b/tests/modules/idr/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/idr/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/idr/test.yml b/tests/modules/idr/test.yml
index 35ee4bc9..9d5ef2a7 100644
--- a/tests/modules/idr/test.yml
+++ b/tests/modules/idr/test.yml
@@ -1,5 +1,5 @@
- name: idr test_idr_narrowpeak
- command: nextflow run tests/modules/idr -entry test_idr_narrowpeak -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/idr -entry test_idr_narrowpeak -c ./tests/config/nextflow.config -c ./tests/modules/idr/nextflow.config
tags:
- idr
files:
@@ -11,7 +11,7 @@
md5sum: 6443507ac66b9d3b64bc56b78328083e
- name: idr test_idr_broadpeak
- command: nextflow run tests/modules/idr -entry test_idr_broadpeak -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/idr -entry test_idr_broadpeak -c ./tests/config/nextflow.config -c ./tests/modules/idr/nextflow.config
tags:
- idr
files:
@@ -23,7 +23,7 @@
md5sum: e6917133112b5cec135c182ffac19237
- name: idr test_idr_noprefix
- command: nextflow run tests/modules/idr -entry test_idr_noprefix -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/idr -entry test_idr_noprefix -c ./tests/config/nextflow.config -c ./tests/modules/idr/nextflow.config
tags:
- idr
files:
diff --git a/tests/modules/imputeme/vcftoprs/main.nf b/tests/modules/imputeme/vcftoprs/main.nf
index ff59ca5e..dccc06e0 100644
--- a/tests/modules/imputeme/vcftoprs/main.nf
+++ b/tests/modules/imputeme/vcftoprs/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { IMPUTEME_VCFTOPRS } from '../../../../modules/imputeme/vcftoprs/main.nf' addParams( options: [:] )
+include { IMPUTEME_VCFTOPRS } from '../../../../modules/imputeme/vcftoprs/main.nf'
workflow test_imputeme_vcftoprs {
diff --git a/tests/modules/imputeme/vcftoprs/nextflow.config b/tests/modules/imputeme/vcftoprs/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/imputeme/vcftoprs/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/imputeme/vcftoprs/test.yml b/tests/modules/imputeme/vcftoprs/test.yml
index efb73769..e5152a03 100644
--- a/tests/modules/imputeme/vcftoprs/test.yml
+++ b/tests/modules/imputeme/vcftoprs/test.yml
@@ -1,5 +1,5 @@
- name: imputeme vcftoprs test_imputeme_vcftoprs
- command: nextflow run tests/modules/imputeme/vcftoprs -entry test_imputeme_vcftoprs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/imputeme/vcftoprs -entry test_imputeme_vcftoprs -c ./tests/config/nextflow.config -c ./tests/modules/imputeme/vcftoprs/nextflow.config
tags:
- imputeme
- imputeme/vcftoprs
diff --git a/tests/modules/iqtree/main.nf b/tests/modules/iqtree/main.nf
index 977d7c0a..2d73bd52 100644
--- a/tests/modules/iqtree/main.nf
+++ b/tests/modules/iqtree/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { IQTREE } from '../../../modules/iqtree/main.nf' addParams( options: [:] )
+include { IQTREE } from '../../../modules/iqtree/main.nf'
workflow test_iqtree {
diff --git a/tests/modules/iqtree/nextflow.config b/tests/modules/iqtree/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/iqtree/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/iqtree/test.yml b/tests/modules/iqtree/test.yml
index e40656a2..06de90d9 100644
--- a/tests/modules/iqtree/test.yml
+++ b/tests/modules/iqtree/test.yml
@@ -1,5 +1,5 @@
- name: iqtree test workflow
- command: nextflow run ./tests/modules/iqtree -entry test_iqtree -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/iqtree -entry test_iqtree -c ./tests/config/nextflow.config -c ./tests/modules/iqtree/nextflow.config
tags:
- iqtree
files:
diff --git a/tests/modules/ismapper/main.nf b/tests/modules/ismapper/main.nf
index b28344dc..abb180f7 100644
--- a/tests/modules/ismapper/main.nf
+++ b/tests/modules/ismapper/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ISMAPPER } from '../../../modules/ismapper/main.nf' addParams( options: [:] )
+include { ISMAPPER } from '../../../modules/ismapper/main.nf'
workflow test_ismapper {
diff --git a/tests/modules/ismapper/nextflow.config b/tests/modules/ismapper/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ismapper/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ismapper/test.yml b/tests/modules/ismapper/test.yml
index 0574b855..b4f64448 100644
--- a/tests/modules/ismapper/test.yml
+++ b/tests/modules/ismapper/test.yml
@@ -1,5 +1,5 @@
- name: ismapper test_ismapper
- command: nextflow run tests/modules/ismapper -entry test_ismapper -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ismapper -entry test_ismapper -c ./tests/config/nextflow.config -c ./tests/modules/ismapper/nextflow.config
tags:
- ismapper
files:
diff --git a/tests/modules/isoseq3/cluster/main.nf b/tests/modules/isoseq3/cluster/main.nf
index 90a24c11..958b03a6 100644
--- a/tests/modules/isoseq3/cluster/main.nf
+++ b/tests/modules/isoseq3/cluster/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ISOSEQ3_CLUSTER } from '../../../../modules/isoseq3/cluster/main.nf' addParams( options: [args: '--singletons --use-qvs --verbose'] )
+include { ISOSEQ3_CLUSTER } from '../../../../modules/isoseq3/cluster/main.nf'
workflow test_isoseq3_cluster {
diff --git a/tests/modules/isoseq3/cluster/nextflow.config b/tests/modules/isoseq3/cluster/nextflow.config
new file mode 100644
index 00000000..8bfeaebd
--- /dev/null
+++ b/tests/modules/isoseq3/cluster/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: ISOSEQ3_CLUSTER {
+ ext.args = '--singletons --use-qvs --verbose'
+ }
+
+}
diff --git a/tests/modules/isoseq3/cluster/test.yml b/tests/modules/isoseq3/cluster/test.yml
index 58b20ae2..b1f12df7 100644
--- a/tests/modules/isoseq3/cluster/test.yml
+++ b/tests/modules/isoseq3/cluster/test.yml
@@ -1,5 +1,5 @@
- name: isoseq3 cluster test_isoseq3_cluster
- command: nextflow run tests/modules/isoseq3/cluster -entry test_isoseq3_cluster -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/isoseq3/cluster -entry test_isoseq3_cluster -c ./tests/config/nextflow.config -c ./tests/modules/isoseq3/cluster/nextflow.config
tags:
- isoseq3
- isoseq3/cluster
diff --git a/tests/modules/isoseq3/refine/main.nf b/tests/modules/isoseq3/refine/main.nf
index 13736604..45dd1560 100644
--- a/tests/modules/isoseq3/refine/main.nf
+++ b/tests/modules/isoseq3/refine/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { ISOSEQ3_REFINE } from '../../../../modules/isoseq3/refine/main' addParams( options: [suffix:'.refine'] )
+include { ISOSEQ3_REFINE } from '../../../../modules/isoseq3/refine/main'
workflow test_isoseq3_refine {
diff --git a/tests/modules/isoseq3/refine/nextflow.config b/tests/modules/isoseq3/refine/nextflow.config
new file mode 100644
index 00000000..88f1bdc4
--- /dev/null
+++ b/tests/modules/isoseq3/refine/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: ISOSEQ3_REFINE {
+ ext.suffix = '.refine'
+ }
+
+}
diff --git a/tests/modules/isoseq3/refine/test.yml b/tests/modules/isoseq3/refine/test.yml
index 2e7782d3..f2c63fda 100644
--- a/tests/modules/isoseq3/refine/test.yml
+++ b/tests/modules/isoseq3/refine/test.yml
@@ -1,5 +1,5 @@
- name: isoseq3 refine test_isoseq3_refine
- command: nextflow run tests/modules/isoseq3/refine -entry test_isoseq3_refine -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/isoseq3/refine -entry test_isoseq3_refine -c ./tests/config/nextflow.config -c ./tests/modules/isoseq3/refine/nextflow.config
tags:
- isoseq3
- isoseq3/refine
diff --git a/tests/modules/ivar/consensus/main.nf b/tests/modules/ivar/consensus/main.nf
index 5e0457b5..d0807984 100644
--- a/tests/modules/ivar/consensus/main.nf
+++ b/tests/modules/ivar/consensus/main.nf
@@ -3,7 +3,7 @@
nextflow.enable.dsl = 2
params.save_mpileup = true
-include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf' addParams( [ options: [args2: '-aa -A -d 0 -Q 0'] ] )
+include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf'
workflow test_ivar_consensus {
input = [ [ id:'test'],
diff --git a/tests/modules/ivar/consensus/nextflow.config b/tests/modules/ivar/consensus/nextflow.config
new file mode 100644
index 00000000..7407619a
--- /dev/null
+++ b/tests/modules/ivar/consensus/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: IVAR_CONSENSUS {
+ ext.args2 = '-aa -A -d 0 -Q 0'
+ }
+
+}
diff --git a/tests/modules/ivar/consensus/test.yml b/tests/modules/ivar/consensus/test.yml
index 071fdc98..caaa640f 100644
--- a/tests/modules/ivar/consensus/test.yml
+++ b/tests/modules/ivar/consensus/test.yml
@@ -1,5 +1,5 @@
- name: ivar consensus
- command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
tags:
- ivar
- ivar/consensus
diff --git a/tests/modules/ivar/trim/main.nf b/tests/modules/ivar/trim/main.nf
index 05b390b0..15d0e739 100644
--- a/tests/modules/ivar/trim/main.nf
+++ b/tests/modules/ivar/trim/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { IVAR_TRIM } from '../../../../modules/ivar/trim/main.nf' addParams([:])
+include { IVAR_TRIM } from '../../../../modules/ivar/trim/main.nf'
workflow test_ivar_trim {
input = [ [ id:'test'],
diff --git a/tests/modules/ivar/trim/nextflow.config b/tests/modules/ivar/trim/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ivar/trim/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ivar/trim/test.yml b/tests/modules/ivar/trim/test.yml
index f2f46676..0be18ba8 100644
--- a/tests/modules/ivar/trim/test.yml
+++ b/tests/modules/ivar/trim/test.yml
@@ -1,5 +1,5 @@
- name: ivar trim
- command: nextflow run ./tests/modules/ivar/trim -entry test_ivar_trim -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ivar/trim -entry test_ivar_trim -c ./tests/config/nextflow.config -c ./tests/modules/ivar/trim/nextflow.config
tags:
- ivar
- ivar/trim
diff --git a/tests/modules/ivar/variants/main.nf b/tests/modules/ivar/variants/main.nf
index 5358e785..f603b5e5 100644
--- a/tests/modules/ivar/variants/main.nf
+++ b/tests/modules/ivar/variants/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf' addParams([:])
+include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf'
workflow test_ivar_variants_no_gff_no_mpileup {
params.gff = false
diff --git a/tests/modules/ivar/variants/nextflow.config b/tests/modules/ivar/variants/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ivar/variants/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ivar/variants/test.yml b/tests/modules/ivar/variants/test.yml
index a8be12a8..00e6e2c0 100644
--- a/tests/modules/ivar/variants/test.yml
+++ b/tests/modules/ivar/variants/test.yml
@@ -1,5 +1,5 @@
- name: ivar variants no gff no mpileup
- command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/ivar/variants/nextflow.config
tags:
- ivar
- ivar/variants
@@ -8,7 +8,7 @@
md5sum: 728f1430f2402861396d9953465ac706
- name: ivar variants no gff with mpileup
- command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config --save_mpileup
+ command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c ./tests/config/nextflow.config --save_mpileup -c ./tests/modules/ivar/variants/nextflow.config
tags:
- ivar
- ivar/variants
@@ -19,7 +19,7 @@
md5sum: 56c4cd5a4ecb7d6364878818f46ae256
- name: ivar variants with gff with mpileup
- command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup
+ command: nextflow run ./tests/modules/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c ./tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup -c ./tests/modules/ivar/variants/nextflow.config
tags:
- ivar
- ivar/variants
diff --git a/tests/modules/jupyternotebook/main.nf b/tests/modules/jupyternotebook/main.nf
index c1da7e11..1db9d812 100644
--- a/tests/modules/jupyternotebook/main.nf
+++ b/tests/modules/jupyternotebook/main.nf
@@ -2,15 +2,9 @@
nextflow.enable.dsl = 2
-include { JUPYTERNOTEBOOK } from '../../../modules/jupyternotebook/main.nf' addParams(
- parametrize: false, options: [:]
-)
-include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/jupyternotebook/main.nf' addParams(
- options: [:]
-)
-include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/jupyternotebook/main.nf' addParams(
- options: [:]
-)
+include { JUPYTERNOTEBOOK } from '../../../modules/jupyternotebook/main.nf'
+include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE } from '../../../modules/jupyternotebook/main.nf'
+include { JUPYTERNOTEBOOK as JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB } from '../../../modules/jupyternotebook/main.nf'
workflow test_jupyternotebook {
diff --git a/tests/modules/jupyternotebook/nextflow.config b/tests/modules/jupyternotebook/nextflow.config
new file mode 100644
index 00000000..6066b2b8
--- /dev/null
+++ b/tests/modules/jupyternotebook/nextflow.config
@@ -0,0 +1,19 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: JUPYTERNOTEBOOK {
+ ext = ['parametrize': false]
+ }
+
+ // this should be the default options, but need to work around
+ // https://github.com/nextflow-io/nextflow/issues/2422
+ withName: JUPYTERNOTEBOOK_PARAMETRIZE {
+ ext = ['parametrize': true]
+ }
+
+ withName: JUPYTERNOTEBOOK_PARAMETRIZE_IPYNB {
+ ext = ['parametrize': true]
+ }
+
+}
diff --git a/tests/modules/jupyternotebook/test.yml b/tests/modules/jupyternotebook/test.yml
index dd4f1175..31fdfdbb 100644
--- a/tests/modules/jupyternotebook/test.yml
+++ b/tests/modules/jupyternotebook/test.yml
@@ -1,5 +1,5 @@
- name: jupyternotebook test_jupyternotebook
- command: nextflow run tests/modules/jupyternotebook -entry test_jupyternotebook -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/jupyternotebook -entry test_jupyternotebook -c ./tests/config/nextflow.config -c ./tests/modules/jupyternotebook/nextflow.config
tags:
- jupyternotebook
files:
@@ -8,7 +8,7 @@
- "n_iter = 10"
- name: jupyternotebook test_jupyternotebook_parametrize
- command: nextflow run tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize -c ./tests/config/nextflow.config -c ./tests/modules/jupyternotebook/nextflow.config
tags:
- jupyternotebook
files:
@@ -19,7 +19,7 @@
- "n_iter = 12"
- name: jupyternotebook test_jupyternotebook_parametrize_ipynb
- command: nextflow run tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize_ipynb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/jupyternotebook -entry test_jupyternotebook_parametrize_ipynb -c ./tests/config/nextflow.config -c ./tests/modules/jupyternotebook/nextflow.config
tags:
- jupyternotebook
files:
diff --git a/tests/modules/kallisto/index/main.nf b/tests/modules/kallisto/index/main.nf
index 7c6078f8..8ecd6d52 100644
--- a/tests/modules/kallisto/index/main.nf
+++ b/tests/modules/kallisto/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf' addParams( options: [:] )
+include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf'
workflow test_kallisto_index {
diff --git a/tests/modules/kallisto/index/nextflow.config b/tests/modules/kallisto/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/kallisto/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/kallisto/index/test.yml b/tests/modules/kallisto/index/test.yml
index b9dd23ad..90a06325 100644
--- a/tests/modules/kallisto/index/test.yml
+++ b/tests/modules/kallisto/index/test.yml
@@ -1,5 +1,5 @@
- name: kallisto index test_kallisto_index
- command: nextflow run tests/modules/kallisto/index -entry test_kallisto_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kallisto/index -entry test_kallisto_index -c ./tests/config/nextflow.config -c ./tests/modules/kallisto/index/nextflow.config
tags:
- kallisto
- kallisto/index
diff --git a/tests/modules/kallistobustools/count/main.nf b/tests/modules/kallistobustools/count/main.nf
index 9172ddfc..6e6be03d 100644
--- a/tests/modules/kallistobustools/count/main.nf
+++ b/tests/modules/kallistobustools/count/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger -m 1"] )
+include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf'
workflow test_kallistobustools_count {
diff --git a/tests/modules/kallistobustools/count/nextflow.config b/tests/modules/kallistobustools/count/nextflow.config
new file mode 100644
index 00000000..eb4e20bd
--- /dev/null
+++ b/tests/modules/kallistobustools/count/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: KALLISTOBUSTOOLS_COUNT {
+ ext.args = '--cellranger -m 1'
+ }
+
+}
diff --git a/tests/modules/kallistobustools/count/test.yml b/tests/modules/kallistobustools/count/test.yml
index 766d5b57..664e9fa6 100644
--- a/tests/modules/kallistobustools/count/test.yml
+++ b/tests/modules/kallistobustools/count/test.yml
@@ -1,5 +1,5 @@
- name: kallistobustools count test_kallistobustools_count
- command: nextflow run tests/modules/kallistobustools/count -entry test_kallistobustools_count -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kallistobustools/count -entry test_kallistobustools_count -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/count/nextflow.config
tags:
- kallistobustools/count
- kallistobustools
diff --git a/tests/modules/kallistobustools/ref/main.nf b/tests/modules/kallistobustools/ref/main.nf
index 31b36d0d..09ea68ea 100644
--- a/tests/modules/kallistobustools/ref/main.nf
+++ b/tests/modules/kallistobustools/ref/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { KALLISTOBUSTOOLS_REF } from '../../../../modules/kallistobustools/ref/main.nf' addParams( options: [:] )
+include { KALLISTOBUSTOOLS_REF } from '../../../../modules/kallistobustools/ref/main.nf'
workflow test_kallistobustools_ref_standard {
diff --git a/tests/modules/kallistobustools/ref/nextflow.config b/tests/modules/kallistobustools/ref/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/kallistobustools/ref/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/kallistobustools/ref/test.yml b/tests/modules/kallistobustools/ref/test.yml
index 54954085..1e8fd6c4 100644
--- a/tests/modules/kallistobustools/ref/test.yml
+++ b/tests/modules/kallistobustools/ref/test.yml
@@ -1,5 +1,5 @@
- name: kallistobustools ref test_kallistobustools_ref_standard
- command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_standard -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_standard -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/ref/nextflow.config
tags:
- kallistobustools/ref
- kallistobustools
@@ -9,7 +9,7 @@
- path: output/kallistobustools/t2g.txt
- name: kallistobustools ref test_kallistobustools_ref_lamanno
- command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_lamanno -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/ref/nextflow.config
tags:
- kallistobustools/ref
- kallistobustools
@@ -22,7 +22,7 @@
- path: output/kallistobustools/t2g.txt
- name: kallistobustools ref test_kallistobustools_ref_nucleus
- command: nextflow run tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kallistobustools/ref -entry test_kallistobustools_ref_nucleus -c ./tests/config/nextflow.config -c ./tests/modules/kallistobustools/ref/nextflow.config
tags:
- kallistobustools/ref
- kallistobustools
diff --git a/tests/modules/khmer/normalizebymedian/main.nf b/tests/modules/khmer/normalizebymedian/main.nf
index 3a3b348c..c439c40f 100644
--- a/tests/modules/khmer/normalizebymedian/main.nf
+++ b/tests/modules/khmer/normalizebymedian/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf' addParams( options: [:] )
-include { KHMER_NORMALIZEBYMEDIAN } from '../../../../modules/khmer/normalizebymedian/main.nf' addParams( options: [:] )
-include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../modules/khmer/normalizebymedian/main.nf' addParams( options: [args: '-C 20 -k 32'] )
+include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf'
+include { KHMER_NORMALIZEBYMEDIAN } from '../../../../modules/khmer/normalizebymedian/main.nf'
+include { KHMER_NORMALIZEBYMEDIAN as KHMER_NORMALIZEBYMEDIAN_ARGS } from '../../../../modules/khmer/normalizebymedian/main.nf'
workflow test_khmer_normalizebymedian_only_pe {
diff --git a/tests/modules/khmer/normalizebymedian/nextflow.config b/tests/modules/khmer/normalizebymedian/nextflow.config
new file mode 100644
index 00000000..279a972a
--- /dev/null
+++ b/tests/modules/khmer/normalizebymedian/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: KHMER_NORMALIZEBYMEDIAN_ARGS {
+ ext.args = '-C 20 -k 32'
+ }
+
+}
diff --git a/tests/modules/khmer/normalizebymedian/test.yml b/tests/modules/khmer/normalizebymedian/test.yml
index a914a8ef..0e61588f 100644
--- a/tests/modules/khmer/normalizebymedian/test.yml
+++ b/tests/modules/khmer/normalizebymedian/test.yml
@@ -1,6 +1,6 @@
# nf-core modules create-test-yml khmer/normalizebymedian
- name: khmer normalizebymedian only pe reads
- command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_pe -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_pe -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
tags:
- khmer
- khmer/normalizebymedian
@@ -10,7 +10,7 @@
#md5sum: 75e05f2e80cf4bd0b534d4b73f7c059c
- name: khmer normalizebymedian only se reads
- command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_se -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_se -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
tags:
- khmer
- khmer/normalizebymedian
@@ -18,7 +18,7 @@
- path: output/khmer/only_se.fastq.gz
- name: khmer normalizebymedian mixed reads
- command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_mixed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_mixed -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
tags:
- khmer
- khmer/normalizebymedian
@@ -26,7 +26,7 @@
- path: output/khmer/mixed.fastq.gz
- name: khmer normalizebymedian multiple pe reads
- command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_multiple_pe -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_multiple_pe -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
tags:
- khmer
- khmer/normalizebymedian
@@ -34,7 +34,7 @@
- path: output/khmer/multiple_pe.fastq.gz
- name: khmer normalizebymedian args
- command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_args -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_args -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config
tags:
- khmer
- khmer/normalizebymedian
diff --git a/tests/modules/kleborate/main.nf b/tests/modules/kleborate/main.nf
index f846e642..bce31225 100644
--- a/tests/modules/kleborate/main.nf
+++ b/tests/modules/kleborate/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { KLEBORATE } from '../../../modules/kleborate/main.nf' addParams( options: [:] )
+include { KLEBORATE } from '../../../modules/kleborate/main.nf'
workflow test_kleborate {
diff --git a/tests/modules/kleborate/nextflow.config b/tests/modules/kleborate/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/kleborate/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/kleborate/test.yml b/tests/modules/kleborate/test.yml
index 1bee4708..c7b25778 100644
--- a/tests/modules/kleborate/test.yml
+++ b/tests/modules/kleborate/test.yml
@@ -1,5 +1,5 @@
- name: kleborate
- command: nextflow run ./tests/modules/kleborate -entry test_kleborate -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kleborate -entry test_kleborate -c ./tests/config/nextflow.config -c ./tests/modules/kleborate/nextflow.config
tags:
- kleborate
files:
diff --git a/tests/modules/kraken2/kraken2/main.nf b/tests/modules/kraken2/kraken2/main.nf
index e5638ec5..12399e9e 100644
--- a/tests/modules/kraken2/kraken2/main.nf
+++ b/tests/modules/kraken2/kraken2/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
-include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf' addParams( options: [:] )
+include { UNTAR } from '../../../../modules/untar/main.nf'
+include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
workflow test_kraken2_kraken2_single_end {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/kraken2/kraken2/nextflow.config b/tests/modules/kraken2/kraken2/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/kraken2/kraken2/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/kraken2/kraken2/test.yml b/tests/modules/kraken2/kraken2/test.yml
index 688fb34c..1ec413bf 100644
--- a/tests/modules/kraken2/kraken2/test.yml
+++ b/tests/modules/kraken2/kraken2/test.yml
@@ -1,5 +1,5 @@
- name: kraken2 kraken2 single-end
- command: nextflow run ./tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_single_end -c ./tests/config/nextflow.config -c ./tests/modules/kraken2/kraken2/nextflow.config
tags:
- kraken2
- kraken2/kraken2
@@ -12,7 +12,7 @@
md5sum: 4227755fe40478b8d7dc8634b489761e
- name: kraken2 kraken2 paired-end
- command: nextflow run ./tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/kraken2/kraken2 -entry test_kraken2_kraken2_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/kraken2/kraken2/nextflow.config
tags:
- kraken2
- kraken2/kraken2
diff --git a/tests/modules/krona/kronadb/main.nf b/tests/modules/krona/kronadb/main.nf
new file mode 100644
index 00000000..ed955854
--- /dev/null
+++ b/tests/modules/krona/kronadb/main.nf
@@ -0,0 +1,9 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KRONADB } from '../../../../modules/krona/kronadb/main.nf'
+
+workflow test_krona_kronadb {
+ KRONA_KRONADB ( )
+}
diff --git a/tests/modules/krona/kronadb/nextflow.config b/tests/modules/krona/kronadb/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/krona/kronadb/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/krona/kronadb/test.yml b/tests/modules/krona/kronadb/test.yml
new file mode 100644
index 00000000..1d61640f
--- /dev/null
+++ b/tests/modules/krona/kronadb/test.yml
@@ -0,0 +1,7 @@
+- name: krona kronadb test_krona_kronadb
+ command: nextflow run ./tests/modules/krona/kronadb -entry test_krona_kronadb -c ./tests/config/nextflow.config -c ./tests/modules/krona/kronadb/nextflow.config
+ tags:
+ - krona
+ - krona/kronadb
+ files:
+ - path: output/krona/taxonomy/taxonomy.tab
diff --git a/tests/modules/krona/ktimporttaxonomy/main.nf b/tests/modules/krona/ktimporttaxonomy/main.nf
new file mode 100644
index 00000000..a23e6fcb
--- /dev/null
+++ b/tests/modules/krona/ktimporttaxonomy/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTIMPORTTAXONOMY } from '../../../../modules/krona/ktimporttaxonomy/main.nf'
+
+workflow test_krona_ktimporttaxonomy {
+
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+ ]
+ taxonomy = file(params.test_data['generic']['txt']['hello'], checkIfExists: true)
+
+ KRONA_KTIMPORTTAXONOMY ( input, taxonomy )
+}
diff --git a/tests/modules/krona/ktimporttaxonomy/nextflow.config b/tests/modules/krona/ktimporttaxonomy/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/krona/ktimporttaxonomy/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/krona/ktimporttaxonomy/test.yml b/tests/modules/krona/ktimporttaxonomy/test.yml
new file mode 100644
index 00000000..b7748980
--- /dev/null
+++ b/tests/modules/krona/ktimporttaxonomy/test.yml
@@ -0,0 +1,9 @@
+- name: krona ktimporttaxonomy test_krona_ktimporttaxonomy
+ command: nextflow run ./tests/modules/krona/ktimporttaxonomy -entry test_krona_ktimporttaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/krona/ktimporttaxonomy/nextflow.config
+ tags:
+ - krona/ktimporttaxonomy
+ - krona
+ files:
+ - path: output/krona/taxonomy.krona.html
+ contains:
+ - "DOCTYPE html PUBLIC"
diff --git a/tests/modules/kronatools/kronadb/main.nf b/tests/modules/kronatools/kronadb/main.nf
deleted file mode 100644
index 90b6e30c..00000000
--- a/tests/modules/kronatools/kronadb/main.nf
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONATOOLS_KRONADB } from '../../../../modules/kronatools/kronadb/main.nf' addParams( options: [:] )
-
-workflow test_kronatools_kronadb {
- KRONATOOLS_KRONADB ( )
-}
diff --git a/tests/modules/kronatools/kronadb/test.yml b/tests/modules/kronatools/kronadb/test.yml
deleted file mode 100644
index 3f346a9d..00000000
--- a/tests/modules/kronatools/kronadb/test.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-- name: kronatools kronadb test_kronatools_kronadb
- command: nextflow run tests/modules/kronatools/kronadb -entry test_kronatools_kronadb -c tests/config/nextflow.config
- tags:
- - kronatools
- - kronatools/kronadb
- files:
- - path: output/kronatools/taxonomy/taxonomy.tab
diff --git a/tests/modules/kronatools/ktimporttaxonomy/main.nf b/tests/modules/kronatools/ktimporttaxonomy/main.nf
deleted file mode 100644
index d7b08a2f..00000000
--- a/tests/modules/kronatools/ktimporttaxonomy/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KRONATOOLS_KTIMPORTTAXONOMY } from '../../../../modules/kronatools/ktimporttaxonomy/main.nf' addParams( options: [:] )
-
-workflow test_kronatools_ktimporttaxonomy {
-
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['generic']['txt']['hello'], checkIfExists: true) ]
-
- taxonomy = [ file(params.test_data['generic']['txt']['hello'] , checkIfExists: true) ]
-
- KRONATOOLS_KTIMPORTTAXONOMY ( input, taxonomy )
-}
diff --git a/tests/modules/kronatools/ktimporttaxonomy/test.yml b/tests/modules/kronatools/ktimporttaxonomy/test.yml
deleted file mode 100644
index 15882b2e..00000000
--- a/tests/modules/kronatools/ktimporttaxonomy/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: kronatools ktimporttaxonomy test_kronatools_ktimporttaxonomy
- command: nextflow run tests/modules/kronatools/ktimporttaxonomy -entry test_kronatools_ktimporttaxonomy -c tests/config/nextflow.config
- tags:
- - kronatools/ktimporttaxonomy
- - kronatools
- files:
- - path: output/kronatools/taxonomy.krona.html
- contains:
- - "DOCTYPE html PUBLIC"
diff --git a/tests/modules/last/dotplot/main.nf b/tests/modules/last/dotplot/main.nf
index b92ed270..3353821d 100644
--- a/tests/modules/last/dotplot/main.nf
+++ b/tests/modules/last/dotplot/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LAST_DOTPLOT } from '../../../../modules/last/dotplot/main.nf' addParams( options: [:] )
+include { LAST_DOTPLOT } from '../../../../modules/last/dotplot/main.nf'
workflow test_last_dotplot {
diff --git a/tests/modules/last/dotplot/nextflow.config b/tests/modules/last/dotplot/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/last/dotplot/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/last/dotplot/test.yml b/tests/modules/last/dotplot/test.yml
index 177e377b..c2a9910f 100644
--- a/tests/modules/last/dotplot/test.yml
+++ b/tests/modules/last/dotplot/test.yml
@@ -1,5 +1,5 @@
- name: last dotplot test_last_dotplot
- command: nextflow run tests/modules/last/dotplot -entry test_last_dotplot -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/dotplot -entry test_last_dotplot -c ./tests/config/nextflow.config -c ./tests/modules/last/dotplot/nextflow.config
tags:
- last/dotplot
- last
diff --git a/tests/modules/last/lastal/main.nf b/tests/modules/last/lastal/main.nf
index 262c8f5f..95c2f917 100644
--- a/tests/modules/last/lastal/main.nf
+++ b/tests/modules/last/lastal/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
-include { LAST_LASTAL } from '../../../../modules/last/lastal/main.nf' addParams( options: [:] )
+include { UNTAR } from '../../../../modules/untar/main.nf'
+include { LAST_LASTAL } from '../../../../modules/last/lastal/main.nf'
workflow test_last_lastal_with_dummy_param_file {
diff --git a/tests/modules/last/lastal/nextflow.config b/tests/modules/last/lastal/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/last/lastal/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/last/lastal/test.yml b/tests/modules/last/lastal/test.yml
index 48b0d223..f75e4ac5 100644
--- a/tests/modules/last/lastal/test.yml
+++ b/tests/modules/last/lastal/test.yml
@@ -1,5 +1,5 @@
- name: last lastal test_last_lastal_with_dummy_param_file
- command: nextflow run tests/modules/last/lastal -entry test_last_lastal_with_dummy_param_file -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/lastal -entry test_last_lastal_with_dummy_param_file -c ./tests/config/nextflow.config -c ./tests/modules/last/lastal/nextflow.config
tags:
- last
- last/lastal
@@ -22,7 +22,7 @@
md5sum: b7c40f06b1309dc6f37849eeb86dfd22
- name: last lastal test_last_lastal_with_real_param_file
- command: nextflow run tests/modules/last/lastal -entry test_last_lastal_with_real_param_file -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/lastal -entry test_last_lastal_with_real_param_file -c ./tests/config/nextflow.config -c ./tests/modules/last/lastal/nextflow.config
tags:
- last
- last/lastal
diff --git a/tests/modules/last/lastdb/main.nf b/tests/modules/last/lastdb/main.nf
index 2f11bee4..d1c7b79a 100644
--- a/tests/modules/last/lastdb/main.nf
+++ b/tests/modules/last/lastdb/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LAST_LASTDB } from '../../../../modules/last/lastdb/main.nf' addParams( options: ['args': '-Q0'] )
+include { LAST_LASTDB } from '../../../../modules/last/lastdb/main.nf'
workflow test_last_lastdb {
diff --git a/tests/modules/last/lastdb/nextflow.config b/tests/modules/last/lastdb/nextflow.config
new file mode 100644
index 00000000..9b8b9878
--- /dev/null
+++ b/tests/modules/last/lastdb/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: LAST_LASTDB {
+ ext.args = '-Q0'
+ }
+
+}
diff --git a/tests/modules/last/lastdb/test.yml b/tests/modules/last/lastdb/test.yml
index c69ecfac..ece44cf3 100644
--- a/tests/modules/last/lastdb/test.yml
+++ b/tests/modules/last/lastdb/test.yml
@@ -1,5 +1,5 @@
- name: last lastdb test_last_lastdb
- command: nextflow run tests/modules/last/lastdb -entry test_last_lastdb -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/lastdb -entry test_last_lastdb -c ./tests/config/nextflow.config -c ./tests/modules/last/lastdb/nextflow.config
tags:
- last/lastdb
- last
@@ -20,7 +20,7 @@
md5sum: b7c40f06b1309dc6f37849eeb86dfd22
- name: last lastdb test_last_lastdb_gzipped_input
- command: nextflow run tests/modules/last/lastdb -entry test_last_lastdb_gzipped_input -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/lastdb -entry test_last_lastdb_gzipped_input -c ./tests/config/nextflow.config -c ./tests/modules/last/lastdb/nextflow.config
tags:
- last/lastdb
- last
diff --git a/tests/modules/last/mafconvert/main.nf b/tests/modules/last/mafconvert/main.nf
index 7864c68a..c87f6e6a 100644
--- a/tests/modules/last/mafconvert/main.nf
+++ b/tests/modules/last/mafconvert/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LAST_MAFCONVERT } from '../../../../modules/last/mafconvert/main.nf' addParams( options: [:] )
+include { LAST_MAFCONVERT } from '../../../../modules/last/mafconvert/main.nf'
workflow test_last_mafconvert {
diff --git a/tests/modules/last/mafconvert/nextflow.config b/tests/modules/last/mafconvert/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/last/mafconvert/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/last/mafconvert/test.yml b/tests/modules/last/mafconvert/test.yml
index 35c65ce9..86a80f20 100644
--- a/tests/modules/last/mafconvert/test.yml
+++ b/tests/modules/last/mafconvert/test.yml
@@ -1,5 +1,5 @@
- name: last mafconvert test_last_mafconvert
- command: nextflow run tests/modules/last/mafconvert -entry test_last_mafconvert -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/mafconvert -entry test_last_mafconvert -c ./tests/config/nextflow.config -c ./tests/modules/last/mafconvert/nextflow.config
tags:
- last/mafconvert
- last
diff --git a/tests/modules/last/mafswap/main.nf b/tests/modules/last/mafswap/main.nf
index 3bb72d63..5cc94932 100644
--- a/tests/modules/last/mafswap/main.nf
+++ b/tests/modules/last/mafswap/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LAST_MAFSWAP } from '../../../../modules/last/mafswap/main.nf' addParams( options: [:] )
+include { LAST_MAFSWAP } from '../../../../modules/last/mafswap/main.nf'
workflow test_last_mafswap {
diff --git a/tests/modules/last/mafswap/nextflow.config b/tests/modules/last/mafswap/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/last/mafswap/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/last/mafswap/test.yml b/tests/modules/last/mafswap/test.yml
index c7e3778d..a0865e00 100644
--- a/tests/modules/last/mafswap/test.yml
+++ b/tests/modules/last/mafswap/test.yml
@@ -1,5 +1,5 @@
- name: last mafswap test_last_mafswap
- command: nextflow run tests/modules/last/mafswap -entry test_last_mafswap -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/mafswap -entry test_last_mafswap -c ./tests/config/nextflow.config -c ./tests/modules/last/mafswap/nextflow.config
tags:
- last
- last/mafswap
diff --git a/tests/modules/last/postmask/main.nf b/tests/modules/last/postmask/main.nf
index c30ac806..9bbb10e9 100644
--- a/tests/modules/last/postmask/main.nf
+++ b/tests/modules/last/postmask/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LAST_POSTMASK } from '../../../../modules/last/postmask/main.nf' addParams( options: [suffix:'.postmask'] )
+include { LAST_POSTMASK } from '../../../../modules/last/postmask/main.nf'
workflow test_last_postmask {
diff --git a/tests/modules/last/postmask/nextflow.config b/tests/modules/last/postmask/nextflow.config
new file mode 100644
index 00000000..dc021264
--- /dev/null
+++ b/tests/modules/last/postmask/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: LAST_POSTMASK {
+ ext.suffix = '.postmask'
+ }
+
+}
diff --git a/tests/modules/last/postmask/test.yml b/tests/modules/last/postmask/test.yml
index 57aea822..81ae7f73 100644
--- a/tests/modules/last/postmask/test.yml
+++ b/tests/modules/last/postmask/test.yml
@@ -1,5 +1,5 @@
- name: last postmask test_last_postmask
- command: nextflow run tests/modules/last/postmask -entry test_last_postmask -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/postmask -entry test_last_postmask -c ./tests/config/nextflow.config -c ./tests/modules/last/postmask/nextflow.config
tags:
- last
- last/postmask
diff --git a/tests/modules/last/split/main.nf b/tests/modules/last/split/main.nf
index 19d899ab..f4ece4f2 100644
--- a/tests/modules/last/split/main.nf
+++ b/tests/modules/last/split/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LAST_SPLIT } from '../../../../modules/last/split/main.nf' addParams( options: ['suffix':'.split'] )
+include { LAST_SPLIT } from '../../../../modules/last/split/main.nf'
workflow test_last_split {
diff --git a/tests/modules/last/split/nextflow.config b/tests/modules/last/split/nextflow.config
new file mode 100644
index 00000000..8b31ca0f
--- /dev/null
+++ b/tests/modules/last/split/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: LAST_SPLIT {
+ ext.suffix = '.split'
+ }
+
+}
diff --git a/tests/modules/last/split/test.yml b/tests/modules/last/split/test.yml
index d57d7477..57eb345f 100644
--- a/tests/modules/last/split/test.yml
+++ b/tests/modules/last/split/test.yml
@@ -1,5 +1,5 @@
- name: last split test_last_split
- command: nextflow run tests/modules/last/split -entry test_last_split -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/split -entry test_last_split -c ./tests/config/nextflow.config -c ./tests/modules/last/split/nextflow.config
tags:
- last
- last/split
diff --git a/tests/modules/last/train/main.nf b/tests/modules/last/train/main.nf
index 26e318c3..0f280a82 100644
--- a/tests/modules/last/train/main.nf
+++ b/tests/modules/last/train/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../../modules/untar/main.nf' addParams( options: [:] )
-include { LAST_TRAIN } from '../../../../modules/last/train/main.nf' addParams( options: [:] )
+include { UNTAR } from '../../../../modules/untar/main.nf'
+include { LAST_TRAIN } from '../../../../modules/last/train/main.nf'
workflow test_last_train {
diff --git a/tests/modules/last/train/nextflow.config b/tests/modules/last/train/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/last/train/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/last/train/test.yml b/tests/modules/last/train/test.yml
index 18eec951..8641600b 100644
--- a/tests/modules/last/train/test.yml
+++ b/tests/modules/last/train/test.yml
@@ -1,5 +1,5 @@
- name: last train test_last_train
- command: nextflow run tests/modules/last/train -entry test_last_train -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/last/train -entry test_last_train -c ./tests/config/nextflow.config -c ./tests/modules/last/train/nextflow.config
tags:
- last/train
- last
diff --git a/tests/modules/leehom/main.nf b/tests/modules/leehom/main.nf
index 2fe6f12f..1615d2e1 100644
--- a/tests/modules/leehom/main.nf
+++ b/tests/modules/leehom/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { LEEHOM } from '../../../modules/leehom/main.nf' addParams( options: [:] )
-include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf' addParams( options: [args: "-f4 -b"] )
+include { LEEHOM } from '../../../modules/leehom/main.nf'
+include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'
workflow test_leehom_bam {
diff --git a/tests/modules/leehom/nextflow.config b/tests/modules/leehom/nextflow.config
new file mode 100644
index 00000000..25df48cd
--- /dev/null
+++ b/tests/modules/leehom/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_VIEW {
+ ext.args = '-f4 -b'
+ }
+
+}
diff --git a/tests/modules/leehom/test.yml b/tests/modules/leehom/test.yml
index 8a9f083e..98257492 100644
--- a/tests/modules/leehom/test.yml
+++ b/tests/modules/leehom/test.yml
@@ -1,17 +1,15 @@
- name: leehom test_leehom_bam
- command: nextflow run tests/modules/leehom -entry test_leehom_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/leehom -entry test_leehom_bam -c ./tests/config/nextflow.config -c ./tests/modules/leehom/nextflow.config
tags:
- leehom
files:
- path: output/leehom/test.bam
- md5sum: 19a1bf95714523868791f1d4d3aaee73
+ - path: output/samtools/test.bam
- path: output/leehom/test.log
md5sum: d1f5da273eb69f41babda510797c7671
- - path: output/samtools/test.bam
- md5sum: 25d13b3b31b147bb3836dea9932c38dd
- name: leehom test_leehom_se_fq
- command: nextflow run tests/modules/leehom -entry test_leehom_se_fq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/leehom -entry test_leehom_se_fq -c ./tests/config/nextflow.config -c ./tests/modules/leehom/nextflow.config
tags:
- leehom
files:
@@ -23,7 +21,7 @@
md5sum: 59aa280cb72dfbea05ba913cb89db143
- name: leehom test_leehom_pe_fq
- command: nextflow run tests/modules/leehom -entry test_leehom_pe_fq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/leehom -entry test_leehom_pe_fq -c ./tests/config/nextflow.config -c ./tests/modules/leehom/nextflow.config
tags:
- leehom
files:
diff --git a/tests/modules/lima/main.nf b/tests/modules/lima/main.nf
index df4b2be2..7501def9 100644
--- a/tests/modules/lima/main.nf
+++ b/tests/modules/lima/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LIMA } from '../../../modules/lima/main.nf' addParams( options: [args: '--isoseq --peek-guess', suffix: ".fl"] )
+include { LIMA } from '../../../modules/lima/main.nf'
workflow test_lima_bam {
diff --git a/tests/modules/lima/nextflow.config b/tests/modules/lima/nextflow.config
new file mode 100644
index 00000000..5091b034
--- /dev/null
+++ b/tests/modules/lima/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: LIMA {
+ ext.args = '--isoseq --peek-guess'
+ ext.suffix = '.fl'
+ }
+
+}
diff --git a/tests/modules/lima/test.yml b/tests/modules/lima/test.yml
index 1ff860d9..8d927624 100644
--- a/tests/modules/lima/test.yml
+++ b/tests/modules/lima/test.yml
@@ -1,5 +1,5 @@
- name: lima test_lima_bam
- command: nextflow run tests/modules/lima -entry test_lima_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lima -entry test_lima_bam -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
tags:
- lima
files:
@@ -23,7 +23,7 @@
md5sum: bcbcaaaca418bdeb91141c81715ca420
- name: lima test_lima_fa
- command: nextflow run tests/modules/lima -entry test_lima_fa -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lima -entry test_lima_fa -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
tags:
- lima
files:
@@ -39,7 +39,7 @@
md5sum: 03be2311ba4afb878d8e547ab38c11eb
- name: lima test_lima_fa_gz
- command: nextflow run tests/modules/lima -entry test_lima_fa_gz -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lima -entry test_lima_fa_gz -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
tags:
- lima
files:
@@ -55,7 +55,7 @@
md5sum: 03be2311ba4afb878d8e547ab38c11eb
- name: lima test_lima_fq
- command: nextflow run tests/modules/lima -entry test_lima_fq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lima -entry test_lima_fq -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
tags:
- lima
files:
@@ -73,7 +73,7 @@
md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
- name: lima test_lima_fq_gz
- command: nextflow run tests/modules/lima -entry test_lima_fq_gz -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lima -entry test_lima_fq_gz -c ./tests/config/nextflow.config -c ./tests/modules/lima/nextflow.config
tags:
- lima
files:
diff --git a/tests/modules/lissero/main.nf b/tests/modules/lissero/main.nf
index e653bd76..339576c3 100644
--- a/tests/modules/lissero/main.nf
+++ b/tests/modules/lissero/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LISSERO } from '../../../modules/lissero/main.nf' addParams( options: [:] )
+include { LISSERO } from '../../../modules/lissero/main.nf'
workflow test_lissero {
diff --git a/tests/modules/lissero/nextflow.config b/tests/modules/lissero/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/lissero/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/lissero/test.yml b/tests/modules/lissero/test.yml
index 19e79623..8dd7339e 100644
--- a/tests/modules/lissero/test.yml
+++ b/tests/modules/lissero/test.yml
@@ -1,5 +1,5 @@
- name: lissero test_lissero
- command: nextflow run tests/modules/lissero -entry test_lissero -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lissero -entry test_lissero -c ./tests/config/nextflow.config -c ./tests/modules/lissero/nextflow.config
tags:
- lissero
files:
diff --git a/tests/modules/lofreq/call/main.nf b/tests/modules/lofreq/call/main.nf
index 2c306fd1..70da4ea5 100644
--- a/tests/modules/lofreq/call/main.nf
+++ b/tests/modules/lofreq/call/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LOFREQ_CALL } from '../../../../modules/lofreq/call/main.nf' addParams( options: [:] )
+include { LOFREQ_CALL } from '../../../../modules/lofreq/call/main.nf'
workflow test_lofreq_call {
diff --git a/tests/modules/lofreq/call/nextflow.config b/tests/modules/lofreq/call/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/lofreq/call/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/lofreq/call/test.yml b/tests/modules/lofreq/call/test.yml
index 88700bfe..b9f42542 100644
--- a/tests/modules/lofreq/call/test.yml
+++ b/tests/modules/lofreq/call/test.yml
@@ -1,5 +1,5 @@
- name: lofreq call test_lofreq_call
- command: nextflow run tests/modules/lofreq/call -entry test_lofreq_call -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lofreq/call -entry test_lofreq_call -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/call/nextflow.config
tags:
- lofreq
- lofreq/call
diff --git a/tests/modules/lofreq/callparallel/main.nf b/tests/modules/lofreq/callparallel/main.nf
index 724bbff1..24ab2db3 100644
--- a/tests/modules/lofreq/callparallel/main.nf
+++ b/tests/modules/lofreq/callparallel/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LOFREQ_CALLPARALLEL } from '../../../../modules/lofreq/callparallel/main.nf' addParams( options: [:] )
+include { LOFREQ_CALLPARALLEL } from '../../../../modules/lofreq/callparallel/main.nf'
workflow test_lofreq_callparallel {
diff --git a/tests/modules/lofreq/callparallel/nextflow.config b/tests/modules/lofreq/callparallel/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/lofreq/callparallel/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/lofreq/callparallel/test.yml b/tests/modules/lofreq/callparallel/test.yml
index e09f68c3..db281012 100644
--- a/tests/modules/lofreq/callparallel/test.yml
+++ b/tests/modules/lofreq/callparallel/test.yml
@@ -1,5 +1,5 @@
- name: lofreq callparallel test_lofreq_callparallel
- command: nextflow run tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lofreq/callparallel -entry test_lofreq_callparallel -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/callparallel/nextflow.config
tags:
- lofreq/callparallel
- lofreq
diff --git a/tests/modules/lofreq/filter/main.nf b/tests/modules/lofreq/filter/main.nf
index c5dcea97..bd2a7f54 100644
--- a/tests/modules/lofreq/filter/main.nf
+++ b/tests/modules/lofreq/filter/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { LOFREQ_FILTER } from '../../../../modules/lofreq/filter/main.nf' addParams( options: [:] )
+include { LOFREQ_FILTER } from '../../../../modules/lofreq/filter/main.nf'
workflow test_lofreq_filter {
diff --git a/tests/modules/lofreq/filter/nextflow.config b/tests/modules/lofreq/filter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/lofreq/filter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/lofreq/filter/test.yml b/tests/modules/lofreq/filter/test.yml
index 4ee82654..d3ee3812 100644
--- a/tests/modules/lofreq/filter/test.yml
+++ b/tests/modules/lofreq/filter/test.yml
@@ -1,5 +1,5 @@
- name: lofreq filter test_lofreq_filter
- command: nextflow run tests/modules/lofreq/filter -entry test_lofreq_filter -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lofreq/filter -entry test_lofreq_filter -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/filter/nextflow.config
tags:
- lofreq
- lofreq/filter
diff --git a/tests/modules/lofreq/indelqual/main.nf b/tests/modules/lofreq/indelqual/main.nf
index ba0493dd..71652ce1 100644
--- a/tests/modules/lofreq/indelqual/main.nf
+++ b/tests/modules/lofreq/indelqual/main.nf
@@ -3,7 +3,7 @@
nextflow.enable.dsl = 2
-include { LOFREQ_INDELQUAL } from '../../../../modules/lofreq/indelqual/main.nf' addParams( options: [ 'args': '--dindel', 'suffix':'.indelqual'] )
+include { LOFREQ_INDELQUAL } from '../../../../modules/lofreq/indelqual/main.nf'
workflow test_lofreq_indelqual {
diff --git a/tests/modules/lofreq/indelqual/nextflow.config b/tests/modules/lofreq/indelqual/nextflow.config
new file mode 100644
index 00000000..b9ad2787
--- /dev/null
+++ b/tests/modules/lofreq/indelqual/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: LOFREQ_INDELQUAL {
+ ext.args = '--dindel'
+ ext.suffix = '.indelqual'
+ }
+
+}
diff --git a/tests/modules/lofreq/indelqual/test.yml b/tests/modules/lofreq/indelqual/test.yml
index f3e73297..6fffb523 100644
--- a/tests/modules/lofreq/indelqual/test.yml
+++ b/tests/modules/lofreq/indelqual/test.yml
@@ -1,5 +1,5 @@
- name: lofreq indelqual
- command: nextflow run ./tests/modules/lofreq/indelqual -entry test_lofreq_indelqual -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/lofreq/indelqual -entry test_lofreq_indelqual -c ./tests/config/nextflow.config -c ./tests/modules/lofreq/indelqual/nextflow.config
tags:
- lofreq
- lofreq/indelqual
diff --git a/tests/modules/macs2/callpeak/main.nf b/tests/modules/macs2/callpeak/main.nf
index db598564..070469dd 100644
--- a/tests/modules/macs2/callpeak/main.nf
+++ b/tests/modules/macs2/callpeak/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
-include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
-include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--format BED --qval 1 --nomodel --extsize 200"] )
+include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf'
+include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/macs2/callpeak/main.nf'
+include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/macs2/callpeak/main.nf'
workflow test_macs2_callpeak_bed {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/macs2/callpeak/nextflow.config b/tests/modules/macs2/callpeak/nextflow.config
new file mode 100644
index 00000000..e3bd3f5d
--- /dev/null
+++ b/tests/modules/macs2/callpeak/nextflow.config
@@ -0,0 +1,17 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: MACS2_CALLPEAK {
+ ext.args = '--qval 0.1'
+ }
+
+ withName: MACS2_CALLPEAK_CTRL {
+ ext.args = '--qval 0.1'
+ }
+
+ withName: MACS2_CALLPEAK_BED {
+ ext.args = '--format BED --qval 1 --nomodel --extsize 200'
+ }
+
+}
diff --git a/tests/modules/macs2/callpeak/test.yml b/tests/modules/macs2/callpeak/test.yml
index 424a9746..43c99140 100644
--- a/tests/modules/macs2/callpeak/test.yml
+++ b/tests/modules/macs2/callpeak/test.yml
@@ -1,5 +1,5 @@
- name: macs2 callpeak test_macs2_callpeak_bed
- command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/macs2/callpeak -entry test_macs2_callpeak_bed -c ./tests/config/nextflow.config -c ./tests/modules/macs2/callpeak/nextflow.config
tags:
- macs2
- macs2/callpeak
@@ -12,7 +12,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: macs2 callpeak test_macs2_callpeak
- command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/macs2/callpeak -entry test_macs2_callpeak -c ./tests/config/nextflow.config -c ./tests/modules/macs2/callpeak/nextflow.config
tags:
- macs2
- macs2/callpeak
@@ -25,7 +25,7 @@
md5sum: 26f0f97b6c14dbca129e947a58067c82
- name: macs2 callpeak test_macs2_callpeak_ctrl
- command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak_ctrl -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/macs2/callpeak -entry test_macs2_callpeak_ctrl -c ./tests/config/nextflow.config -c ./tests/modules/macs2/callpeak/nextflow.config
tags:
- macs2
- macs2/callpeak
diff --git a/tests/modules/malt/build_test/main.nf b/tests/modules/malt/build_test/main.nf
index b2f3eaf6..2542da0c 100644
--- a/tests/modules/malt/build_test/main.nf
+++ b/tests/modules/malt/build_test/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { UNZIP } from '../../../../modules/unzip/main.nf' addParams( options: [:] )
-include { MALT_BUILD } from '../../../../modules/malt/build/main.nf' addParams( options: [:] )
+include { UNZIP } from '../../../../modules/unzip/main.nf'
+include { MALT_BUILD } from '../../../../modules/malt/build/main.nf'
workflow test_malt_build {
fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/malt/build_test/nextflow.config b/tests/modules/malt/build_test/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/malt/build_test/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/malt/build_test/test.yml b/tests/modules/malt/build_test/test.yml
index c3ed4b8f..c6694ad5 100644
--- a/tests/modules/malt/build_test/test.yml
+++ b/tests/modules/malt/build_test/test.yml
@@ -1,5 +1,5 @@
- name: malt build
- command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build -c ./tests/config/nextflow.config -c ./tests/modules/malt/build/nextflow.config
tags:
- malt
- malt/build
@@ -21,7 +21,7 @@
- path: output/malt/malt_index/taxonomy.tre
md5sum: bde26a1fff5c63d3046d3863607a1e70
- name: malt build gff
- command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build_gff -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build_gff -c ./tests/config/nextflow.config -c ./tests/modules/malt/build/nextflow.config
tags:
- malt
- malt/build
diff --git a/tests/modules/malt/run/main.nf b/tests/modules/malt/run/main.nf
index 6292ca61..292a3fcf 100644
--- a/tests/modules/malt/run/main.nf
+++ b/tests/modules/malt/run/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { UNZIP } from '../../../../modules/unzip/main.nf' addParams( options: [:] )
-include { MALT_BUILD } from '../../../../modules/malt/build/main.nf' addParams( options: [:] )
-include { MALT_RUN } from '../../../../modules/malt/run/main.nf' addParams( options: [:] )
+include { UNZIP } from '../../../../modules/unzip/main.nf'
+include { MALT_BUILD } from '../../../../modules/malt/build/main.nf'
+include { MALT_RUN } from '../../../../modules/malt/run/main.nf'
workflow test_malt_run {
diff --git a/tests/modules/malt/run/nextflow.config b/tests/modules/malt/run/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/malt/run/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/malt/run/test.yml b/tests/modules/malt/run/test.yml
index 0c245f2f..5b0742e4 100644
--- a/tests/modules/malt/run/test.yml
+++ b/tests/modules/malt/run/test.yml
@@ -1,5 +1,5 @@
- name: malt run
- command: nextflow run ./tests/modules/malt/run -entry test_malt_run -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/malt/run -entry test_malt_run -c ./tests/config/nextflow.config -c ./tests/modules/malt/run/nextflow.config
tags:
- malt
- malt/run
diff --git a/tests/modules/maltextract/main.nf b/tests/modules/maltextract/main.nf
index d18923ca..8e0a2241 100644
--- a/tests/modules/maltextract/main.nf
+++ b/tests/modules/maltextract/main.nf
@@ -2,11 +2,11 @@
nextflow.enable.dsl = 2
-include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf' addParams( options: [:] )
-include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf' addParams( options: [:] )
-include { MALT_BUILD } from '../../../modules/malt/build/main.nf' addParams( options: [:] )
-include { MALT_RUN } from '../../../modules/malt/run/main.nf' addParams( options: [:] )
-include { MALTEXTRACT } from '../../../modules/maltextract/main.nf' addParams( options: [:] )
+include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf'
+include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf'
+include { MALT_BUILD } from '../../../modules/malt/build/main.nf'
+include { MALT_RUN } from '../../../modules/malt/run/main.nf'
+include { MALTEXTRACT } from '../../../modules/maltextract/main.nf'
workflow test_maltextract {
diff --git a/tests/modules/maltextract/nextflow.config b/tests/modules/maltextract/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/maltextract/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/maltextract/test.yml b/tests/modules/maltextract/test.yml
index 87bf0182..2440c100 100644
--- a/tests/modules/maltextract/test.yml
+++ b/tests/modules/maltextract/test.yml
@@ -1,5 +1,5 @@
- name: maltextract
- command: nextflow run ./tests/modules/maltextract -entry test_maltextract -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/maltextract -entry test_maltextract -c ./tests/config/nextflow.config -c ./tests/modules/maltextract/nextflow.config
tags:
- maltextract
files:
diff --git a/tests/modules/manta/germline/main.nf b/tests/modules/manta/germline/main.nf
index df996464..f8adedb0 100644
--- a/tests/modules/manta/germline/main.nf
+++ b/tests/modules/manta/germline/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf' addParams( options: [:] )
+include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
workflow test_manta_germline {
input = [
diff --git a/tests/modules/manta/germline/nextflow.config b/tests/modules/manta/germline/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/manta/germline/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/manta/germline/test.yml b/tests/modules/manta/germline/test.yml
index b4086d76..c6ead9eb 100644
--- a/tests/modules/manta/germline/test.yml
+++ b/tests/modules/manta/germline/test.yml
@@ -1,5 +1,5 @@
- name: manta germline
- command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
tags:
- manta
- manta/germline
@@ -11,7 +11,7 @@
- path: output/manta/test.diploid_sv.vcf.gz
- path: output/manta/test.diploid_sv.vcf.gz.tbi
- name: manta germline target bed
- command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config
tags:
- manta
- manta/germline
diff --git a/tests/modules/manta/somatic/main.nf b/tests/modules/manta/somatic/main.nf
index 553735c9..7da41bea 100644
--- a/tests/modules/manta/somatic/main.nf
+++ b/tests/modules/manta/somatic/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MANTA_SOMATIC } from '../../../../modules/manta/somatic/main.nf' addParams( options: [:] )
+include { MANTA_SOMATIC } from '../../../../modules/manta/somatic/main.nf'
workflow test_manta_somatic {
diff --git a/tests/modules/manta/somatic/nextflow.config b/tests/modules/manta/somatic/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/manta/somatic/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/manta/somatic/test.yml b/tests/modules/manta/somatic/test.yml
index 72f0953d..d701a210 100644
--- a/tests/modules/manta/somatic/test.yml
+++ b/tests/modules/manta/somatic/test.yml
@@ -1,5 +1,5 @@
- name: manta somatic test_manta_somatic
- command: nextflow run tests/modules/manta/somatic -entry test_manta_somatic -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/manta/somatic -entry test_manta_somatic -c ./tests/config/nextflow.config -c ./tests/modules/manta/somatic/nextflow.config
tags:
- manta/somatic
- manta
diff --git a/tests/modules/manta/tumoronly/main.nf b/tests/modules/manta/tumoronly/main.nf
index 436ab781..be0d3dbb 100644
--- a/tests/modules/manta/tumoronly/main.nf
+++ b/tests/modules/manta/tumoronly/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf' addParams( options: [:] )
+include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf'
workflow test_manta_tumoronly {
input = [
diff --git a/tests/modules/manta/tumoronly/nextflow.config b/tests/modules/manta/tumoronly/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/manta/tumoronly/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/manta/tumoronly/test.yml b/tests/modules/manta/tumoronly/test.yml
index 13f2cde1..c56e23fa 100644
--- a/tests/modules/manta/tumoronly/test.yml
+++ b/tests/modules/manta/tumoronly/test.yml
@@ -1,5 +1,5 @@
- name: manta tumoronly
- command: nextflow run ./tests/modules/manta/tumoronly -entry test_manta_tumoronly -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/manta/tumoronly -entry test_manta_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/manta/tumoronly/nextflow.config
tags:
- manta
- manta/tumoronly
@@ -11,7 +11,7 @@
- path: output/manta/test.tumor_sv.vcf.gz
- path: output/manta/test.tumor_sv.vcf.gz.tbi
- name: manta tumoronly target bed
- command: nextflow run ./tests/modules/manta/tumoronly -entry test_manta_tumoronly_target_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/manta/tumoronly -entry test_manta_tumoronly_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/manta/tumoronly/nextflow.config
tags:
- manta
- manta/tumoronly
diff --git a/tests/modules/mapdamage2/main.nf b/tests/modules/mapdamage2/main.nf
index a4a0eb02..b7e4d23b 100644
--- a/tests/modules/mapdamage2/main.nf
+++ b/tests/modules/mapdamage2/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MAPDAMAGE2 } from '../../../modules/mapdamage2/main.nf' addParams( options: [:] )
+include { MAPDAMAGE2 } from '../../../modules/mapdamage2/main.nf'
workflow test_mapdamage2 {
diff --git a/tests/modules/mapdamage2/nextflow.config b/tests/modules/mapdamage2/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mapdamage2/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mapdamage2/test.yml b/tests/modules/mapdamage2/test.yml
index 657f59b5..96c8b2da 100644
--- a/tests/modules/mapdamage2/test.yml
+++ b/tests/modules/mapdamage2/test.yml
@@ -1,5 +1,5 @@
- name: mapdamage2 test_mapdamage2
- command: nextflow run tests/modules/mapdamage2 -entry test_mapdamage2 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mapdamage2 -entry test_mapdamage2 -c ./tests/config/nextflow.config -c ./tests/modules/mapdamage2/nextflow.config
tags:
- mapdamage2
files:
diff --git a/tests/modules/mash/sketch/main.nf b/tests/modules/mash/sketch/main.nf
index da72d1e3..cec2035b 100644
--- a/tests/modules/mash/sketch/main.nf
+++ b/tests/modules/mash/sketch/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MASH_SKETCH } from '../../../../modules/mash/sketch/main.nf' addParams( options: [:] )
+include { MASH_SKETCH } from '../../../../modules/mash/sketch/main.nf'
workflow test_mash_sketch {
diff --git a/tests/modules/mash/sketch/nextflow.config b/tests/modules/mash/sketch/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mash/sketch/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mash/sketch/test.yml b/tests/modules/mash/sketch/test.yml
index 78f4598b..d5039956 100644
--- a/tests/modules/mash/sketch/test.yml
+++ b/tests/modules/mash/sketch/test.yml
@@ -1,5 +1,5 @@
- name: mash sketch
- command: nextflow run ./tests/modules/mash/sketch -entry test_mash_sketch -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mash/sketch -entry test_mash_sketch -c ./tests/config/nextflow.config -c ./tests/modules/mash/sketch/nextflow.config
tags:
- mash/sketch
files:
diff --git a/tests/modules/mashtree/main.nf b/tests/modules/mashtree/main.nf
index 47a7c12a..07f5e561 100644
--- a/tests/modules/mashtree/main.nf
+++ b/tests/modules/mashtree/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MASHTREE } from '../../../modules/mashtree/main.nf' addParams( options: [:] )
+include { MASHTREE } from '../../../modules/mashtree/main.nf'
workflow test_mashtree {
diff --git a/tests/modules/mashtree/nextflow.config b/tests/modules/mashtree/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mashtree/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mashtree/test.yml b/tests/modules/mashtree/test.yml
index 83ff6272..bea9638c 100644
--- a/tests/modules/mashtree/test.yml
+++ b/tests/modules/mashtree/test.yml
@@ -1,5 +1,5 @@
- name: mashtree test_mashtree
- command: nextflow run tests/modules/mashtree -entry test_mashtree -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mashtree -entry test_mashtree -c ./tests/config/nextflow.config -c ./tests/modules/mashtree/nextflow.config
tags:
- mashtree
files:
diff --git a/tests/modules/maxbin2/main.nf b/tests/modules/maxbin2/main.nf
index bede2c6a..3df417be 100644
--- a/tests/modules/maxbin2/main.nf
+++ b/tests/modules/maxbin2/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MAXBIN2 } from '../../../modules/maxbin2/main.nf' addParams( options: [:] )
+include { MAXBIN2 } from '../../../modules/maxbin2/main.nf'
workflow test_maxbin2 {
diff --git a/tests/modules/maxbin2/nextflow.config b/tests/modules/maxbin2/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/maxbin2/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/maxbin2/test.yml b/tests/modules/maxbin2/test.yml
index 2721d17a..a8ba98f9 100644
--- a/tests/modules/maxbin2/test.yml
+++ b/tests/modules/maxbin2/test.yml
@@ -1,5 +1,5 @@
- name: maxbin2
- command: nextflow run ./tests/modules/maxbin2 -entry test_maxbin2 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/maxbin2 -entry test_maxbin2 -c ./tests/config/nextflow.config -c ./tests/modules/maxbin2/nextflow.config
tags:
- maxbin2
files:
diff --git a/tests/modules/medaka/main.nf b/tests/modules/medaka/main.nf
index 300e086b..75fc135b 100644
--- a/tests/modules/medaka/main.nf
+++ b/tests/modules/medaka/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MEDAKA } from '../../../modules/medaka/main.nf' addParams( options: [suffix:'.polished.genome'] )
+include { MEDAKA } from '../../../modules/medaka/main.nf'
workflow test_medaka {
diff --git a/tests/modules/medaka/nextflow.config b/tests/modules/medaka/nextflow.config
new file mode 100644
index 00000000..1f89be62
--- /dev/null
+++ b/tests/modules/medaka/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: MEDAKA {
+ ext.suffix = '.polished.genome'
+ }
+
+}
diff --git a/tests/modules/medaka/test.yml b/tests/modules/medaka/test.yml
index 9ce5521e..54146bdc 100644
--- a/tests/modules/medaka/test.yml
+++ b/tests/modules/medaka/test.yml
@@ -1,5 +1,5 @@
- name: medaka test_medaka
- command: nextflow run ./tests/modules/medaka -entry test_medaka -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/medaka -entry test_medaka -c ./tests/config/nextflow.config -c ./tests/modules/medaka/nextflow.config
tags:
- medaka
files:
diff --git a/tests/modules/megahit/main.nf b/tests/modules/megahit/main.nf
index dcf07cd6..88acf3e3 100644
--- a/tests/modules/megahit/main.nf
+++ b/tests/modules/megahit/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MEGAHIT } from '../../../modules/megahit/main.nf' addParams( options: [:] )
+include { MEGAHIT } from '../../../modules/megahit/main.nf'
workflow test_megahit {
diff --git a/tests/modules/megahit/nextflow.config b/tests/modules/megahit/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/megahit/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/megahit/test.yml b/tests/modules/megahit/test.yml
index c390891b..2072ac12 100644
--- a/tests/modules/megahit/test.yml
+++ b/tests/modules/megahit/test.yml
@@ -1,5 +1,5 @@
- name: megahit
- command: nextflow run ./tests/modules/megahit -entry test_megahit -c tests/config/nextflow.config -process.cpus 1
+ command: nextflow run ./tests/modules/megahit -entry test_megahit -c ./tests/config/nextflow.config -process.cpus 1 -c ./tests/modules/megahit/nextflow.config
tags:
- megahit
files:
@@ -31,7 +31,7 @@
md5sum: 7029066c27ac6f5ef18d660d5741979a
- name: megahit_single
- command: nextflow run ./tests/modules/megahit -entry test_megahit_single -c tests/config/nextflow.config -process.cpus 1
+ command: nextflow run ./tests/modules/megahit -entry test_megahit_single -c ./tests/config/nextflow.config -process.cpus 1 -c ./tests/modules/megahit/nextflow.config
tags:
- megahit
files:
diff --git a/tests/modules/meningotype/main.nf b/tests/modules/meningotype/main.nf
index d660ec72..a2d0ff10 100644
--- a/tests/modules/meningotype/main.nf
+++ b/tests/modules/meningotype/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MENINGOTYPE } from '../../../modules/meningotype/main.nf' addParams( options: [:] )
+include { MENINGOTYPE } from '../../../modules/meningotype/main.nf'
workflow test_meningotype {
diff --git a/tests/modules/meningotype/nextflow.config b/tests/modules/meningotype/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/meningotype/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/meningotype/test.yml b/tests/modules/meningotype/test.yml
index c61e78a6..02ec8e1f 100644
--- a/tests/modules/meningotype/test.yml
+++ b/tests/modules/meningotype/test.yml
@@ -1,5 +1,5 @@
- name: meningotype test_meningotype
- command: nextflow run tests/modules/meningotype -entry test_meningotype -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/meningotype -entry test_meningotype -c ./tests/config/nextflow.config -c ./tests/modules/meningotype/nextflow.config
tags:
- meningotype
files:
diff --git a/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf b/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf
index 2cfc2e2c..00309402 100644
--- a/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf
+++ b/tests/modules/metabat2/jgisummarizebamcontigdepths/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' addParams( options: [:] )
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
workflow test_metabat2_jgisummarizebamcontigdepths {
diff --git a/tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config b/tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml b/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml
index d318c6d4..86c49d26 100644
--- a/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml
+++ b/tests/modules/metabat2/jgisummarizebamcontigdepths/test.yml
@@ -1,5 +1,5 @@
- name: metabat2 jgisummarizebamcontigdepths test_metabat2_jgisummarizebamcontigdepths
- command: nextflow run tests/modules/metabat2/jgisummarizebamcontigdepths -entry test_metabat2_jgisummarizebamcontigdepths -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metabat2/jgisummarizebamcontigdepths -entry test_metabat2_jgisummarizebamcontigdepths -c ./tests/config/nextflow.config -c ./tests/modules/metabat2/jgisummarizebamcontigdepths/nextflow.config
tags:
- metabat2/jgisummarizebamcontigdepths
- metabat2
diff --git a/tests/modules/metabat2/metabat2/main.nf b/tests/modules/metabat2/metabat2/main.nf
index 3d01f194..0179e4c3 100644
--- a/tests/modules/metabat2/metabat2/main.nf
+++ b/tests/modules/metabat2/metabat2/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf' addParams( options: [args: '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'] )
-include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf' addParams( options: [:] )
+include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
+include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
workflow test_metabat2_no_depth {
diff --git a/tests/modules/metabat2/metabat2/nextflow.config b/tests/modules/metabat2/metabat2/nextflow.config
new file mode 100644
index 00000000..83754d8b
--- /dev/null
+++ b/tests/modules/metabat2/metabat2/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: METABAT2_METABAT2 {
+ ext.args = '--minContig 1500 --minCV 0.1 --minCVSum 0.1 --minClsSize 10 --minS 2'
+ }
+
+}
diff --git a/tests/modules/metabat2/metabat2/test.yml b/tests/modules/metabat2/metabat2/test.yml
index 7b3435b7..1a8660a7 100644
--- a/tests/modules/metabat2/metabat2/test.yml
+++ b/tests/modules/metabat2/metabat2/test.yml
@@ -1,5 +1,5 @@
- name: metabat2 metabat2 test_metabat2_no_depth
- command: nextflow run tests/modules/metabat2/metabat2 -entry test_metabat2_no_depth -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metabat2/metabat2 -entry test_metabat2_no_depth -c ./tests/config/nextflow.config -c ./tests/modules/metabat2/metabat2/nextflow.config
tags:
- metabat2/metabat2
- metabat2
@@ -10,7 +10,7 @@
md5sum: ea77e8c4426d2337419905b57f1ec335
- name: metabat2 metabat2 test_metabat2_depth
- command: nextflow run tests/modules/metabat2/metabat2 -entry test_metabat2_depth -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metabat2/metabat2 -entry test_metabat2_depth -c ./tests/config/nextflow.config -c ./tests/modules/metabat2/metabat2/nextflow.config
tags:
- metabat2/metabat2
- metabat2
diff --git a/tests/modules/metaphlan3/main.nf b/tests/modules/metaphlan3/main.nf
index 2d855683..3354d2d9 100644
--- a/tests/modules/metaphlan3/main.nf
+++ b/tests/modules/metaphlan3/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../modules/untar/main.nf' addParams( options: [:] )
-include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf' addParams( options: ['suffix': '.sam'] )
-include { METAPHLAN3 } from '../../../modules/metaphlan3/main.nf' addParams( options: [ 'args':'--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local' ] )
+include { UNTAR } from '../../../modules/untar/main.nf'
+include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf'
+include { METAPHLAN3 } from '../../../modules/metaphlan3/main.nf'
workflow test_metaphlan3_single_end {
@@ -42,7 +42,7 @@ workflow test_metaphlan3_sam {
UNTAR ( db )
- SAMTOOLS_VIEW ( input )
+ SAMTOOLS_VIEW ( input, [] )
METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar )
}
diff --git a/tests/modules/metaphlan3/nextflow.config b/tests/modules/metaphlan3/nextflow.config
new file mode 100644
index 00000000..2dde2212
--- /dev/null
+++ b/tests/modules/metaphlan3/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_VIEW {
+ ext.suffix = '.sam'
+ }
+
+ withName: METAPHLAN3 {
+ ext.args = '--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local'
+ }
+
+}
diff --git a/tests/modules/metaphlan3/test.yml b/tests/modules/metaphlan3/test.yml
index fbd5e70b..92e731d2 100644
--- a/tests/modules/metaphlan3/test.yml
+++ b/tests/modules/metaphlan3/test.yml
@@ -1,5 +1,5 @@
- name: metaphlan3 test_metaphlan3_single_end
- command: nextflow run tests/modules/metaphlan3 -entry test_metaphlan3_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_single_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
tags:
- metaphlan3
files:
@@ -30,7 +30,7 @@
md5sum: 1ca16b905abf657b88ca2bc12e7ad404
- name: metaphlan3 test_metaphlan3_paired_end
- command: nextflow run tests/modules/metaphlan3 -entry test_metaphlan3_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
tags:
- metaphlan3
files:
@@ -61,7 +61,7 @@
md5sum: 1ca16b905abf657b88ca2bc12e7ad404
- name: metaphlan3 test_metaphlan3_sam
- command: nextflow run tests/modules/metaphlan3 -entry test_metaphlan3_sam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_sam -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
tags:
- metaphlan3
files:
@@ -92,7 +92,7 @@
md5sum: 1ca16b905abf657b88ca2bc12e7ad404
- name: metaphlan3 test_metaphlan3_fasta
- command: nextflow run tests/modules/metaphlan3 -entry test_metaphlan3_fasta -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/metaphlan3 -entry test_metaphlan3_fasta -c ./tests/config/nextflow.config -c ./tests/modules/metaphlan3/nextflow.config
tags:
- metaphlan3
files:
diff --git a/tests/modules/methyldackel/extract/main.nf b/tests/modules/methyldackel/extract/main.nf
index 40e87b0b..92f92308 100644
--- a/tests/modules/methyldackel/extract/main.nf
+++ b/tests/modules/methyldackel/extract/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { METHYLDACKEL_EXTRACT } from '../../../../modules/methyldackel/extract/main.nf' addParams( options: [:] )
+include { METHYLDACKEL_EXTRACT } from '../../../../modules/methyldackel/extract/main.nf'
workflow test_methyldackel_extract {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/methyldackel/extract/nextflow.config b/tests/modules/methyldackel/extract/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/methyldackel/extract/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/methyldackel/extract/test.yml b/tests/modules/methyldackel/extract/test.yml
index 70c371d7..28f969f3 100644
--- a/tests/modules/methyldackel/extract/test.yml
+++ b/tests/modules/methyldackel/extract/test.yml
@@ -1,5 +1,5 @@
- name: methyldackel extract
- command: nextflow run ./tests/modules/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/methyldackel/extract -entry test_methyldackel_extract -c ./tests/config/nextflow.config -c ./tests/modules/methyldackel/extract/nextflow.config
tags:
- methyldackel
- methyldackel/extract
diff --git a/tests/modules/methyldackel/mbias/main.nf b/tests/modules/methyldackel/mbias/main.nf
index 318dd663..f304e22f 100644
--- a/tests/modules/methyldackel/mbias/main.nf
+++ b/tests/modules/methyldackel/mbias/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { METHYLDACKEL_MBIAS } from '../../../../modules/methyldackel/mbias/main.nf' addParams( options: [:] )
+include { METHYLDACKEL_MBIAS } from '../../../../modules/methyldackel/mbias/main.nf'
workflow test_methyldackel_mbias {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/methyldackel/mbias/nextflow.config b/tests/modules/methyldackel/mbias/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/methyldackel/mbias/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/methyldackel/mbias/test.yml b/tests/modules/methyldackel/mbias/test.yml
index 43074291..8bb23f24 100644
--- a/tests/modules/methyldackel/mbias/test.yml
+++ b/tests/modules/methyldackel/mbias/test.yml
@@ -1,5 +1,5 @@
- name: methyldackel mbias
- command: nextflow run ./tests/modules/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/methyldackel/mbias -entry test_methyldackel_mbias -c ./tests/config/nextflow.config -c ./tests/modules/methyldackel/mbias/nextflow.config
tags:
- methyldackel
- methyldackel/mbias
diff --git a/tests/modules/minia/main.nf b/tests/modules/minia/main.nf
index e23f5cc4..5be4d17f 100644
--- a/tests/modules/minia/main.nf
+++ b/tests/modules/minia/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MINIA } from '../../../modules/minia/main.nf' addParams( options: [:] )
+include { MINIA } from '../../../modules/minia/main.nf'
workflow test_minia {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/minia/nextflow.config b/tests/modules/minia/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/minia/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/minia/test.yml b/tests/modules/minia/test.yml
index 6836f51d..78b84f37 100644
--- a/tests/modules/minia/test.yml
+++ b/tests/modules/minia/test.yml
@@ -1,5 +1,5 @@
- name: minia
- command: nextflow run tests/modules/minia -entry test_minia -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/minia -entry test_minia -c ./tests/config/nextflow.config -c ./tests/modules/minia/nextflow.config
tags:
- minia
files:
diff --git a/tests/modules/miniasm/main.nf b/tests/modules/miniasm/main.nf
index f3d23d56..949660ac 100644
--- a/tests/modules/miniasm/main.nf
+++ b/tests/modules/miniasm/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MINIASM } from '../../../modules/miniasm/main.nf' addParams( options: [suffix:'.assembly'] )
+include { MINIASM } from '../../../modules/miniasm/main.nf'
workflow test_miniasm {
diff --git a/tests/modules/miniasm/nextflow.config b/tests/modules/miniasm/nextflow.config
new file mode 100644
index 00000000..844a0120
--- /dev/null
+++ b/tests/modules/miniasm/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: MINIASM {
+ ext.suffix = '.assembly'
+ }
+
+}
diff --git a/tests/modules/miniasm/test.yml b/tests/modules/miniasm/test.yml
index 7596a269..0bdc350a 100644
--- a/tests/modules/miniasm/test.yml
+++ b/tests/modules/miniasm/test.yml
@@ -1,5 +1,5 @@
- name: miniasm test_miniasm
- command: nextflow run tests/modules/miniasm -entry test_miniasm -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/miniasm -entry test_miniasm -c ./tests/config/nextflow.config -c ./tests/modules/miniasm/nextflow.config
tags:
- miniasm
files:
diff --git a/tests/modules/minimap2/align/main.nf b/tests/modules/minimap2/align/main.nf
index b4dbf5bd..e507d3e5 100644
--- a/tests/modules/minimap2/align/main.nf
+++ b/tests/modules/minimap2/align/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MINIMAP2_ALIGN } from '../../../../modules/minimap2/align/main.nf' addParams( options: [:] )
+include { MINIMAP2_ALIGN } from '../../../../modules/minimap2/align/main.nf'
workflow test_minimap2_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/minimap2/align/nextflow.config b/tests/modules/minimap2/align/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/minimap2/align/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml
index 3309bf4b..598a5d25 100644
--- a/tests/modules/minimap2/align/test.yml
+++ b/tests/modules/minimap2/align/test.yml
@@ -1,5 +1,5 @@
- name: minimap2 align single-end
- command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
tags:
- minimap2
- minimap2/align
@@ -8,7 +8,7 @@
md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
- name: minimap2 align paired-end
- command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
tags:
- minimap2
- minimap2/align
diff --git a/tests/modules/minimap2/index/main.nf b/tests/modules/minimap2/index/main.nf
index 39aa93e0..a69efa85 100644
--- a/tests/modules/minimap2/index/main.nf
+++ b/tests/modules/minimap2/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MINIMAP2_INDEX } from '../../../../modules/minimap2/index/main.nf' addParams( options: [:] )
+include { MINIMAP2_INDEX } from '../../../../modules/minimap2/index/main.nf'
workflow test_minimap2_index {
diff --git a/tests/modules/minimap2/index/nextflow.config b/tests/modules/minimap2/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/minimap2/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/minimap2/index/test.yml b/tests/modules/minimap2/index/test.yml
index 7a3cc8fa..95700452 100644
--- a/tests/modules/minimap2/index/test.yml
+++ b/tests/modules/minimap2/index/test.yml
@@ -1,5 +1,5 @@
- name: minimap2 index
- command: nextflow run ./tests/modules/minimap2/index -entry test_minimap2_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/minimap2/index -entry test_minimap2_index -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/index/nextflow.config
tags:
- minimap2
- minimap2/index
diff --git a/tests/modules/mlst/main.nf b/tests/modules/mlst/main.nf
index 4b7d44be..f84ec622 100644
--- a/tests/modules/mlst/main.nf
+++ b/tests/modules/mlst/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MLST } from '../../../modules/mlst/main.nf' addParams( options: [:] )
+include { MLST } from '../../../modules/mlst/main.nf'
workflow test_mlst {
diff --git a/tests/modules/mlst/nextflow.config b/tests/modules/mlst/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mlst/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mlst/test.yml b/tests/modules/mlst/test.yml
index 5a7c7a0e..53eacc5a 100644
--- a/tests/modules/mlst/test.yml
+++ b/tests/modules/mlst/test.yml
@@ -1,5 +1,5 @@
- name: mlst test_mlst
- command: nextflow run tests/modules/mlst -entry test_mlst -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mlst -entry test_mlst -c ./tests/config/nextflow.config -c ./tests/modules/mlst/nextflow.config
tags:
- mlst
files:
diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf
index c4d8e9c4..8862204d 100644
--- a/tests/modules/mosdepth/main.nf
+++ b/tests/modules/mosdepth/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' addParams( options: [:] )
+include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
workflow test_mosdepth {
input = [ [ id:'test', single_end:true ],
diff --git a/tests/modules/mosdepth/nextflow.config b/tests/modules/mosdepth/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mosdepth/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml
index f5ab5608..e264ef3b 100644
--- a/tests/modules/mosdepth/test.yml
+++ b/tests/modules/mosdepth/test.yml
@@ -1,5 +1,5 @@
- name: mosdepth
- command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
tags:
- mosdepth
files:
diff --git a/tests/modules/msisensor/msi/main.nf b/tests/modules/msisensor/msi/main.nf
index f8ce4187..259ec887 100644
--- a/tests/modules/msisensor/msi/main.nf
+++ b/tests/modules/msisensor/msi/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf' addParams( options: [:] )
-include { MSISENSOR_MSI } from '../../../../modules/msisensor/msi/main.nf' addParams( options: [:] )
+include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf'
+include { MSISENSOR_MSI } from '../../../../modules/msisensor/msi/main.nf'
workflow test_msisensor_msi {
diff --git a/tests/modules/msisensor/msi/nextflow.config b/tests/modules/msisensor/msi/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/msisensor/msi/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/msisensor/msi/test.yml b/tests/modules/msisensor/msi/test.yml
index 1fc74ad3..0d0da1ee 100644
--- a/tests/modules/msisensor/msi/test.yml
+++ b/tests/modules/msisensor/msi/test.yml
@@ -1,5 +1,5 @@
- name: msisensor msi
- command: nextflow run ./tests/modules/msisensor/msi -entry test_msisensor_msi -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/msisensor/msi -entry test_msisensor_msi -c ./tests/config/nextflow.config -c ./tests/modules/msisensor/msi/nextflow.config
tags:
- msisensor
- msisensor/msi
diff --git a/tests/modules/msisensor/scan/main.nf b/tests/modules/msisensor/scan/main.nf
index 2303d0b9..de46dd9b 100644
--- a/tests/modules/msisensor/scan/main.nf
+++ b/tests/modules/msisensor/scan/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf' addParams( options: [:] )
+include { MSISENSOR_SCAN } from '../../../../modules/msisensor/scan/main.nf'
workflow test_msisensor_scan {
diff --git a/tests/modules/msisensor/scan/nextflow.config b/tests/modules/msisensor/scan/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/msisensor/scan/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/msisensor/scan/test.yml b/tests/modules/msisensor/scan/test.yml
index 0d28c5a2..9e697a59 100644
--- a/tests/modules/msisensor/scan/test.yml
+++ b/tests/modules/msisensor/scan/test.yml
@@ -1,5 +1,5 @@
- name: msisensor scan
- command: nextflow run ./tests/modules/msisensor/scan -entry test_msisensor_scan -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/msisensor/scan -entry test_msisensor_scan -c ./tests/config/nextflow.config -c ./tests/modules/msisensor/scan/nextflow.config
tags:
- msisensor
- msisensor/scan
diff --git a/tests/modules/mtnucratio/main.nf b/tests/modules/mtnucratio/main.nf
index dd9fc9db..6d6f5e1d 100644
--- a/tests/modules/mtnucratio/main.nf
+++ b/tests/modules/mtnucratio/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MTNUCRATIO } from '../../../modules/mtnucratio/main.nf' addParams( options: [:] )
+include { MTNUCRATIO } from '../../../modules/mtnucratio/main.nf'
workflow test_mtnucratio {
diff --git a/tests/modules/mtnucratio/nextflow.config b/tests/modules/mtnucratio/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mtnucratio/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mtnucratio/test.yml b/tests/modules/mtnucratio/test.yml
index 76cbaf32..24dc3d16 100644
--- a/tests/modules/mtnucratio/test.yml
+++ b/tests/modules/mtnucratio/test.yml
@@ -1,5 +1,5 @@
- name: mtnucratio
- command: nextflow run tests/modules/mtnucratio -entry test_mtnucratio -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mtnucratio -entry test_mtnucratio -c ./tests/config/nextflow.config -c ./tests/modules/mtnucratio/nextflow.config
tags:
- mtnucratio
files:
diff --git a/tests/modules/multiqc/main.nf b/tests/modules/multiqc/main.nf
index ddabb43a..43643985 100644
--- a/tests/modules/multiqc/main.nf
+++ b/tests/modules/multiqc/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { FASTQC } from '../../../modules/fastqc/main.nf' addParams( options: [:] )
-include { MULTIQC } from '../../../modules/multiqc/main.nf' addParams( options: [:] )
+include { FASTQC } from '../../../modules/fastqc/main.nf'
+include { MULTIQC } from '../../../modules/multiqc/main.nf'
workflow test_multiqc {
input = [ [ id: 'test', single_end: false ],
diff --git a/tests/modules/multiqc/nextflow.config b/tests/modules/multiqc/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/multiqc/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/multiqc/test.yml b/tests/modules/multiqc/test.yml
index 69ded5d5..39796872 100644
--- a/tests/modules/multiqc/test.yml
+++ b/tests/modules/multiqc/test.yml
@@ -1,5 +1,5 @@
- name: multiqc
- command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/multiqc -entry test_multiqc -c ./tests/config/nextflow.config -c ./tests/modules/multiqc/nextflow.config
tags:
- multiqc
files:
diff --git a/tests/modules/mummer/main.nf b/tests/modules/mummer/main.nf
index b24f8b16..30c8c4b8 100644
--- a/tests/modules/mummer/main.nf
+++ b/tests/modules/mummer/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { MUMMER } from '../../../modules/mummer/main.nf' addParams( options: [:] )
+include { MUMMER } from '../../../modules/mummer/main.nf'
workflow test_mummer {
diff --git a/tests/modules/mummer/nextflow.config b/tests/modules/mummer/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/mummer/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/mummer/test.yml b/tests/modules/mummer/test.yml
index 1d368d14..359fd4ad 100644
--- a/tests/modules/mummer/test.yml
+++ b/tests/modules/mummer/test.yml
@@ -1,5 +1,5 @@
- name: mummer test_mummer
- command: nextflow run tests/modules/mummer -entry test_mummer -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/mummer -entry test_mummer -c ./tests/config/nextflow.config -c ./tests/modules/mummer/nextflow.config
tags:
- mummer
files:
diff --git a/tests/modules/muscle/main.nf b/tests/modules/muscle/main.nf
index 81a71761..a6294519 100644
--- a/tests/modules/muscle/main.nf
+++ b/tests/modules/muscle/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { MUSCLE } from '../../../modules/muscle/main.nf' addParams( options: ['args': '-fasta -verbose -phys -phyi -maxiters 2'])
-include { MUSCLE as MUSCLE_TREE } from '../../../modules/muscle/main.nf' addParams( options: ['args': '-maketree'])
+include { MUSCLE } from '../../../modules/muscle/main.nf'
+include { MUSCLE as MUSCLE_TREE } from '../../../modules/muscle/main.nf'
workflow test_muscle {
diff --git a/tests/modules/muscle/nextflow.config b/tests/modules/muscle/nextflow.config
new file mode 100644
index 00000000..31331b0f
--- /dev/null
+++ b/tests/modules/muscle/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: MUSCLE {
+ ext.args = '-fasta -verbose -phys -phyi -maxiters 2'
+ }
+
+ withName: MUSCLE_TREE {
+ ext.args = '-maketree'
+ }
+
+}
diff --git a/tests/modules/muscle/test.yml b/tests/modules/muscle/test.yml
index 7f9d2a54..6995d71d 100644
--- a/tests/modules/muscle/test.yml
+++ b/tests/modules/muscle/test.yml
@@ -1,5 +1,5 @@
- name: muscle test_muscle
- command: nextflow run tests/modules/muscle -entry test_muscle -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/muscle -entry test_muscle -c ./tests/config/nextflow.config -c ./tests/modules/muscle/nextflow.config
tags:
- muscle
files:
diff --git a/tests/modules/nanolyse/main.nf b/tests/modules/nanolyse/main.nf
index 97941a6d..91013cd0 100644
--- a/tests/modules/nanolyse/main.nf
+++ b/tests/modules/nanolyse/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { NANOLYSE } from '../../../modules/nanolyse/main.nf' addParams( options: [suffix: '.clean'] )
+include { NANOLYSE } from '../../../modules/nanolyse/main.nf'
workflow test_nanolyse {
input = [
diff --git a/tests/modules/nanolyse/nextflow.config b/tests/modules/nanolyse/nextflow.config
new file mode 100644
index 00000000..ede080cc
--- /dev/null
+++ b/tests/modules/nanolyse/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: NANOLYSE {
+ ext.suffix = '.clean'
+ }
+
+}
diff --git a/tests/modules/nanolyse/test.yml b/tests/modules/nanolyse/test.yml
index 4938fe57..5af2e65e 100644
--- a/tests/modules/nanolyse/test.yml
+++ b/tests/modules/nanolyse/test.yml
@@ -1,5 +1,5 @@
- name: nanolyse
- command: nextflow run ./tests/modules/nanolyse -entry test_nanolyse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/nanolyse -entry test_nanolyse -c ./tests/config/nextflow.config -c ./tests/modules/nanolyse/nextflow.config
tags:
- nanolyse
files:
diff --git a/tests/modules/nanoplot/main.nf b/tests/modules/nanoplot/main.nf
index a483f5e2..04c923c2 100644
--- a/tests/modules/nanoplot/main.nf
+++ b/tests/modules/nanoplot/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { NANOPLOT } from '../../../modules/nanoplot/main.nf' addParams( options: [:] )
+include { NANOPLOT } from '../../../modules/nanoplot/main.nf'
workflow test_nanoplot_summary {
def input = []
diff --git a/tests/modules/nanoplot/nextflow.config b/tests/modules/nanoplot/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/nanoplot/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nanoplot/test.yml b/tests/modules/nanoplot/test.yml
index 475b90c9..6549953e 100644
--- a/tests/modules/nanoplot/test.yml
+++ b/tests/modules/nanoplot/test.yml
@@ -1,6 +1,6 @@
- name: nanoplot_summary
- command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_summary -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_summary -c ./tests/config/nextflow.config -c ./tests/modules/nanoplot/nextflow.config
tags:
- nanoplot
files:
@@ -8,7 +8,7 @@
contains:
- "report"
- name: nanoplot_fastq
- command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_fastq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_fastq -c ./tests/config/nextflow.config -c ./tests/modules/nanoplot/nextflow.config
tags:
- nanoplot
files:
diff --git a/tests/modules/ncbigenomedownload/main.nf b/tests/modules/ncbigenomedownload/main.nf
index f729b91d..2447b97c 100644
--- a/tests/modules/ncbigenomedownload/main.nf
+++ b/tests/modules/ncbigenomedownload/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { NCBIGENOMEDOWNLOAD } from '../../../modules/ncbigenomedownload/main.nf' addParams( options: [ args: '-A GCF_000013425.1 --formats genbank,fasta,assembly-stats bacteria '] )
+include { NCBIGENOMEDOWNLOAD } from '../../../modules/ncbigenomedownload/main.nf'
workflow test_ncbigenomedownload {
diff --git a/tests/modules/ncbigenomedownload/nextflow.config b/tests/modules/ncbigenomedownload/nextflow.config
new file mode 100644
index 00000000..7e6ccf70
--- /dev/null
+++ b/tests/modules/ncbigenomedownload/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: NCBIGENOMEDOWNLOAD {
+ ext.args = '-A GCF_000013425.1 --formats genbank,fasta,assembly-stats bacteria'
+ }
+}
diff --git a/tests/modules/ncbigenomedownload/test.yml b/tests/modules/ncbigenomedownload/test.yml
index 7d1f7c74..8765e04f 100644
--- a/tests/modules/ncbigenomedownload/test.yml
+++ b/tests/modules/ncbigenomedownload/test.yml
@@ -1,5 +1,5 @@
- name: ncbigenomedownload test_ncbigenomedownload
- command: nextflow run tests/modules/ncbigenomedownload -entry test_ncbigenomedownload -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ncbigenomedownload -entry test_ncbigenomedownload -c ./tests/config/nextflow.config -c ./tests/modules/ncbigenomedownload/nextflow.config
tags:
- ncbigenomedownload
files:
diff --git a/tests/modules/nextclade/main.nf b/tests/modules/nextclade/main.nf
index 93c50ca5..15750990 100755
--- a/tests/modules/nextclade/main.nf
+++ b/tests/modules/nextclade/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { NEXTCLADE } from '../../../modules/nextclade/main.nf' addParams( options: [:] )
+include { NEXTCLADE } from '../../../modules/nextclade/main.nf'
workflow test_nextclade {
input = [
diff --git a/tests/modules/nextclade/nextflow.config b/tests/modules/nextclade/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/nextclade/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nextclade/test.yml b/tests/modules/nextclade/test.yml
index 4d1d7743..36218aad 100755
--- a/tests/modules/nextclade/test.yml
+++ b/tests/modules/nextclade/test.yml
@@ -1,5 +1,5 @@
- name: nextclade test_nextclade
- command: nextflow run tests/modules/nextclade -entry test_nextclade -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/nextclade -entry test_nextclade -c ./tests/config/nextflow.config -c ./tests/modules/nextclade/nextflow.config
tags:
- nextclade
files:
diff --git a/tests/modules/ngmaster/main.nf b/tests/modules/ngmaster/main.nf
index 8bc975ed..b23530bc 100644
--- a/tests/modules/ngmaster/main.nf
+++ b/tests/modules/ngmaster/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { NGMASTER } from '../../../modules/ngmaster/main.nf' addParams( options: [:] )
+include { NGMASTER } from '../../../modules/ngmaster/main.nf'
workflow test_ngmaster {
diff --git a/tests/modules/ngmaster/nextflow.config b/tests/modules/ngmaster/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ngmaster/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ngmaster/test.yml b/tests/modules/ngmaster/test.yml
index 31584a54..fb8dec82 100644
--- a/tests/modules/ngmaster/test.yml
+++ b/tests/modules/ngmaster/test.yml
@@ -1,5 +1,5 @@
- name: ngmaster test_ngmaster
- command: nextflow run tests/modules/ngmaster -entry test_ngmaster -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ngmaster -entry test_ngmaster -c ./tests/config/nextflow.config -c ./tests/modules/ngmaster/nextflow.config
tags:
- ngmaster
files:
diff --git a/tests/modules/nucmer/main.nf b/tests/modules/nucmer/main.nf
index 8021f577..98e74b07 100644
--- a/tests/modules/nucmer/main.nf
+++ b/tests/modules/nucmer/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { NUCMER } from '../../../modules/nucmer/main.nf' addParams( options: [:] )
+include { NUCMER } from '../../../modules/nucmer/main.nf'
workflow test_nucmer {
diff --git a/tests/modules/nucmer/nextflow.config b/tests/modules/nucmer/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/nucmer/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nucmer/test.yml b/tests/modules/nucmer/test.yml
index 86b3df5d..62caced4 100644
--- a/tests/modules/nucmer/test.yml
+++ b/tests/modules/nucmer/test.yml
@@ -1,5 +1,5 @@
- name: nucmer test_nucmer
- command: nextflow run tests/modules/nucmer -entry test_nucmer -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/nucmer -entry test_nucmer -c ./tests/config/nextflow.config -c ./tests/modules/nucmer/nextflow.config
tags:
- nucmer
files:
diff --git a/tests/modules/optitype/main.nf b/tests/modules/optitype/main.nf
index c27a5c99..55b46f0a 100644
--- a/tests/modules/optitype/main.nf
+++ b/tests/modules/optitype/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { OPTITYPE } from '../../../modules/optitype/main.nf' addParams( options: ['args':'-e 1 -b 0.009', 'args2':'solver=glpk'] )
+include { OPTITYPE } from '../../../modules/optitype/main.nf'
workflow test_optitype {
input = [ [ id:'test', seq_type:'dna' ], // meta map
diff --git a/tests/modules/optitype/nextflow.config b/tests/modules/optitype/nextflow.config
new file mode 100644
index 00000000..14ad9e3f
--- /dev/null
+++ b/tests/modules/optitype/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: OPTITYPE {
+ ext.args = '-e 1 -b 0.009'
+ ext.args2 = 'solver=glpk'
+ }
+
+}
diff --git a/tests/modules/optitype/test.yml b/tests/modules/optitype/test.yml
index 41f35988..7c2ff0d0 100644
--- a/tests/modules/optitype/test.yml
+++ b/tests/modules/optitype/test.yml
@@ -1,5 +1,5 @@
- name: optitype test_optitype
- command: nextflow run tests/modules/optitype -entry test_optitype -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/optitype -entry test_optitype -c ./tests/config/nextflow.config -c ./tests/modules/optitype/nextflow.config
tags:
- optitype
files:
diff --git a/tests/modules/pairix/main.nf b/tests/modules/pairix/main.nf
index f1e2a44a..474bacbb 100644
--- a/tests/modules/pairix/main.nf
+++ b/tests/modules/pairix/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRIX } from '../../../modules/pairix/main.nf' addParams( options: [:] )
+include { PAIRIX } from '../../../modules/pairix/main.nf'
workflow test_pairix {
diff --git a/tests/modules/pairix/nextflow.config b/tests/modules/pairix/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pairix/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pairix/test.yml b/tests/modules/pairix/test.yml
index 304a94b3..4cd9d37d 100644
--- a/tests/modules/pairix/test.yml
+++ b/tests/modules/pairix/test.yml
@@ -1,5 +1,5 @@
- name: pairix test_pairix
- command: nextflow run tests/modules/pairix -entry test_pairix -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairix -entry test_pairix -c ./tests/config/nextflow.config -c ./tests/modules/pairix/nextflow.config
tags:
- pairix
files:
diff --git a/tests/modules/pairtools/dedup/main.nf b/tests/modules/pairtools/dedup/main.nf
index 2c10c85b..28121526 100644
--- a/tests/modules/pairtools/dedup/main.nf
+++ b/tests/modules/pairtools/dedup/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRTOOLS_DEDUP } from '../../../../modules/pairtools/dedup/main.nf' addParams( options: ['suffix':'.dedup'] )
+include { PAIRTOOLS_DEDUP } from '../../../../modules/pairtools/dedup/main.nf'
workflow test_pairtools_dedup {
diff --git a/tests/modules/pairtools/dedup/nextflow.config b/tests/modules/pairtools/dedup/nextflow.config
new file mode 100644
index 00000000..1de3348f
--- /dev/null
+++ b/tests/modules/pairtools/dedup/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PAIRTOOLS_DEDUP {
+ ext.suffix = '.dedup'
+ }
+
+}
diff --git a/tests/modules/pairtools/dedup/test.yml b/tests/modules/pairtools/dedup/test.yml
index 25fc51f7..6d7f99f4 100644
--- a/tests/modules/pairtools/dedup/test.yml
+++ b/tests/modules/pairtools/dedup/test.yml
@@ -1,5 +1,5 @@
- name: pairtools dedup test_pairtools_dedup
- command: nextflow run tests/modules/pairtools/dedup -entry test_pairtools_dedup -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairtools/dedup -entry test_pairtools_dedup -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/dedup/nextflow.config
tags:
- pairtools/dedup
- pairtools
diff --git a/tests/modules/pairtools/flip/main.nf b/tests/modules/pairtools/flip/main.nf
index ed980102..e4d740e2 100644
--- a/tests/modules/pairtools/flip/main.nf
+++ b/tests/modules/pairtools/flip/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRTOOLS_FLIP } from '../../../../modules/pairtools/flip/main.nf' addParams( options: [:] )
+include { PAIRTOOLS_FLIP } from '../../../../modules/pairtools/flip/main.nf'
workflow test_pairtools_flip {
diff --git a/tests/modules/pairtools/flip/nextflow.config b/tests/modules/pairtools/flip/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pairtools/flip/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pairtools/flip/test.yml b/tests/modules/pairtools/flip/test.yml
index eeef6530..cec54976 100644
--- a/tests/modules/pairtools/flip/test.yml
+++ b/tests/modules/pairtools/flip/test.yml
@@ -1,5 +1,5 @@
- name: pairtools flip test_pairtools_flip
- command: nextflow run tests/modules/pairtools/flip -entry test_pairtools_flip -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairtools/flip -entry test_pairtools_flip -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/flip/nextflow.config
tags:
- pairtools/flip
- pairtools
diff --git a/tests/modules/pairtools/parse/main.nf b/tests/modules/pairtools/parse/main.nf
index 26ceaa4f..f006fd6a 100644
--- a/tests/modules/pairtools/parse/main.nf
+++ b/tests/modules/pairtools/parse/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRTOOLS_PARSE } from '../../../../modules/pairtools/parse/main.nf' addParams( options: ['suffix':'.raw'] )
+include { PAIRTOOLS_PARSE } from '../../../../modules/pairtools/parse/main.nf'
workflow test_pairtools_parse {
diff --git a/tests/modules/pairtools/parse/nextflow.config b/tests/modules/pairtools/parse/nextflow.config
new file mode 100644
index 00000000..1a1182f6
--- /dev/null
+++ b/tests/modules/pairtools/parse/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PAIRTOOLS_PARSE {
+ ext.suffix = '.raw'
+ }
+
+}
diff --git a/tests/modules/pairtools/parse/test.yml b/tests/modules/pairtools/parse/test.yml
index e5d18e01..cf01038c 100644
--- a/tests/modules/pairtools/parse/test.yml
+++ b/tests/modules/pairtools/parse/test.yml
@@ -1,5 +1,5 @@
- name: pairtools parse test_pairtools_parse
- command: nextflow run tests/modules/pairtools/parse -entry test_pairtools_parse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairtools/parse -entry test_pairtools_parse -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/parse/nextflow.config
tags:
- pairtools
- pairtools/parse
diff --git a/tests/modules/pairtools/restrict/main.nf b/tests/modules/pairtools/restrict/main.nf
index f785ed88..ae7e328b 100644
--- a/tests/modules/pairtools/restrict/main.nf
+++ b/tests/modules/pairtools/restrict/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRTOOLS_RESTRICT } from '../../../../modules/pairtools/restrict/main.nf' addParams( options: ['suffix':'.restrict'] )
+include { PAIRTOOLS_RESTRICT } from '../../../../modules/pairtools/restrict/main.nf'
workflow test_pairtools_restrict {
diff --git a/tests/modules/pairtools/restrict/nextflow.config b/tests/modules/pairtools/restrict/nextflow.config
new file mode 100644
index 00000000..857d7534
--- /dev/null
+++ b/tests/modules/pairtools/restrict/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PAIRTOOLS_RESTRICT {
+ ext.suffix = '.restrict'
+ }
+
+}
diff --git a/tests/modules/pairtools/restrict/test.yml b/tests/modules/pairtools/restrict/test.yml
index afc64930..484b3739 100644
--- a/tests/modules/pairtools/restrict/test.yml
+++ b/tests/modules/pairtools/restrict/test.yml
@@ -1,5 +1,5 @@
- name: pairtools restrict test_pairtools_restrict
- command: nextflow run tests/modules/pairtools/restrict -entry test_pairtools_restrict -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairtools/restrict -entry test_pairtools_restrict -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/restrict/nextflow.config
tags:
- pairtools/restrict
- pairtools
diff --git a/tests/modules/pairtools/select/main.nf b/tests/modules/pairtools/select/main.nf
index 2efd29c7..ff65cd95 100644
--- a/tests/modules/pairtools/select/main.nf
+++ b/tests/modules/pairtools/select/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRTOOLS_SELECT } from '../../../../modules/pairtools/select/main.nf' addParams( options: [args:"(pair_type == 'RU') or (pair_type == 'UR') or (pair_type == 'UU')"] )
+include { PAIRTOOLS_SELECT } from '../../../../modules/pairtools/select/main.nf'
workflow test_pairtools_select {
diff --git a/tests/modules/pairtools/select/nextflow.config b/tests/modules/pairtools/select/nextflow.config
new file mode 100644
index 00000000..df33cd2e
--- /dev/null
+++ b/tests/modules/pairtools/select/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PAIRTOOLS_SELECT {
+ ext.args = "(pair_type == \'RU\') or (pair_type == \'UR\') or (pair_type == \'UU\')"
+ }
+
+}
diff --git a/tests/modules/pairtools/select/test.yml b/tests/modules/pairtools/select/test.yml
index adeb50c3..431e8366 100644
--- a/tests/modules/pairtools/select/test.yml
+++ b/tests/modules/pairtools/select/test.yml
@@ -1,5 +1,5 @@
- name: pairtools select test_pairtools_select
- command: nextflow run tests/modules/pairtools/select -entry test_pairtools_select -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairtools/select -entry test_pairtools_select -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/select/nextflow.config
tags:
- pairtools/select
- pairtools
diff --git a/tests/modules/pairtools/sort/main.nf b/tests/modules/pairtools/sort/main.nf
index dfb505e0..0e484c76 100644
--- a/tests/modules/pairtools/sort/main.nf
+++ b/tests/modules/pairtools/sort/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PAIRTOOLS_SORT } from '../../../../modules/pairtools/sort/main.nf' addParams( options: ['suffix':'.sorted'] )
+include { PAIRTOOLS_SORT } from '../../../../modules/pairtools/sort/main.nf'
workflow test_pairtools_sort {
diff --git a/tests/modules/pairtools/sort/nextflow.config b/tests/modules/pairtools/sort/nextflow.config
new file mode 100644
index 00000000..86b3d802
--- /dev/null
+++ b/tests/modules/pairtools/sort/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PAIRTOOLS_SORT {
+ ext.suffix = '.sorted'
+ }
+
+}
diff --git a/tests/modules/pairtools/sort/test.yml b/tests/modules/pairtools/sort/test.yml
index 9eea74a0..4d4866aa 100644
--- a/tests/modules/pairtools/sort/test.yml
+++ b/tests/modules/pairtools/sort/test.yml
@@ -1,5 +1,5 @@
- name: pairtools sort test_pairtools_sort
- command: nextflow run tests/modules/pairtools/sort -entry test_pairtools_sort -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pairtools/sort -entry test_pairtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/pairtools/sort/nextflow.config
tags:
- pairtools/sort
- pairtools
diff --git a/tests/modules/pangolin/main.nf b/tests/modules/pangolin/main.nf
index b8130c5d..ab4aa4af 100644
--- a/tests/modules/pangolin/main.nf
+++ b/tests/modules/pangolin/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PANGOLIN } from '../../../modules/pangolin/main.nf' addParams( options: [:] )
+include { PANGOLIN } from '../../../modules/pangolin/main.nf'
workflow test_pangolin {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/pangolin/nextflow.config b/tests/modules/pangolin/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pangolin/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pangolin/test.yml b/tests/modules/pangolin/test.yml
index 5fb5e79e..c77e4912 100644
--- a/tests/modules/pangolin/test.yml
+++ b/tests/modules/pangolin/test.yml
@@ -1,5 +1,5 @@
- name: pangolin
- command: nextflow run ./tests/modules/pangolin -entry test_pangolin -c ./tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pangolin -entry test_pangolin -c ./tests/config/nextflow.config -c ./tests/modules/pangolin/nextflow.config
tags:
- pangolin
files:
diff --git a/tests/modules/paraclu/main.nf b/tests/modules/paraclu/main.nf
index f5101591..3bd75dc0 100644
--- a/tests/modules/paraclu/main.nf
+++ b/tests/modules/paraclu/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PARACLU } from '../../../modules/paraclu/main.nf' addParams( options: [:] )
+include { PARACLU } from '../../../modules/paraclu/main.nf'
workflow test_paraclu {
diff --git a/tests/modules/paraclu/nextflow.config b/tests/modules/paraclu/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/paraclu/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/paraclu/test.yml b/tests/modules/paraclu/test.yml
index 3aa3e8b4..36b37df5 100644
--- a/tests/modules/paraclu/test.yml
+++ b/tests/modules/paraclu/test.yml
@@ -1,5 +1,5 @@
- name: paraclu test_paraclu
- command: nextflow run tests/modules/paraclu -entry test_paraclu -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/paraclu -entry test_paraclu -c ./tests/config/nextflow.config -c ./tests/modules/paraclu/nextflow.config
tags:
- paraclu
files:
diff --git a/tests/modules/pbbam/pbmerge/main.nf b/tests/modules/pbbam/pbmerge/main.nf
index 9220af0c..34ed33a6 100644
--- a/tests/modules/pbbam/pbmerge/main.nf
+++ b/tests/modules/pbbam/pbmerge/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PBBAM_PBMERGE } from '../../../../modules/pbbam/pbmerge/main.nf' addParams( options: [suffix: '.merged'] )
+include { PBBAM_PBMERGE } from '../../../../modules/pbbam/pbmerge/main.nf'
workflow test_pbbam_pbmerge {
diff --git a/tests/modules/pbbam/pbmerge/nextflow.config b/tests/modules/pbbam/pbmerge/nextflow.config
new file mode 100644
index 00000000..c897068b
--- /dev/null
+++ b/tests/modules/pbbam/pbmerge/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PBBAM_PBMERGE {
+ ext.suffix = '.merged'
+ }
+
+}
diff --git a/tests/modules/pbbam/pbmerge/test.yml b/tests/modules/pbbam/pbmerge/test.yml
index 4f334c0e..0a6d7da3 100644
--- a/tests/modules/pbbam/pbmerge/test.yml
+++ b/tests/modules/pbbam/pbmerge/test.yml
@@ -1,5 +1,5 @@
- name: pbbam pbmerge test_pbbam_pbmerge
- command: nextflow run tests/modules/pbbam/pbmerge -entry test_pbbam_pbmerge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pbbam/pbmerge -entry test_pbbam_pbmerge -c ./tests/config/nextflow.config -c ./tests/modules/pbbam/pbmerge/nextflow.config
tags:
- pbbam/pbmerge
- pbbam
diff --git a/tests/modules/pbccs/main.nf b/tests/modules/pbccs/main.nf
index 74c1b864..91a2ab30 100644
--- a/tests/modules/pbccs/main.nf
+++ b/tests/modules/pbccs/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PBCCS } from '../../../modules/pbccs/main.nf' addParams( options: [args:'--min-rq 0.9'] )
+include { PBCCS } from '../../../modules/pbccs/main.nf'
workflow test_pbccs {
diff --git a/tests/modules/pbccs/nextflow.config b/tests/modules/pbccs/nextflow.config
new file mode 100644
index 00000000..869909ce
--- /dev/null
+++ b/tests/modules/pbccs/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PBCCS {
+ ext.args = '--min-rq 0.9'
+ }
+
+}
diff --git a/tests/modules/pbccs/test.yml b/tests/modules/pbccs/test.yml
index af225eb1..5d481923 100644
--- a/tests/modules/pbccs/test.yml
+++ b/tests/modules/pbccs/test.yml
@@ -1,5 +1,5 @@
- name: pbccs test_pbccs
- command: nextflow run tests/modules/pbccs -entry test_pbccs -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pbccs -entry test_pbccs -c ./tests/config/nextflow.config -c ./tests/modules/pbccs/nextflow.config
tags:
- pbccs
files:
diff --git a/tests/modules/peddy/main.nf b/tests/modules/peddy/main.nf
index d6331752..e53e8152 100644
--- a/tests/modules/peddy/main.nf
+++ b/tests/modules/peddy/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PEDDY } from '../../../modules/peddy/main.nf' addParams( options: [:] )
+include { PEDDY } from '../../../modules/peddy/main.nf'
workflow test_peddy {
@@ -13,5 +13,5 @@ workflow test_peddy {
]
ped = file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true)
- PEDDY ( input , ped )
+ PEDDY ( input, ped )
}
diff --git a/tests/modules/peddy/nextflow.config b/tests/modules/peddy/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/peddy/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/peddy/test.yml b/tests/modules/peddy/test.yml
index 77bf00f6..0ed6dc94 100644
--- a/tests/modules/peddy/test.yml
+++ b/tests/modules/peddy/test.yml
@@ -1,5 +1,5 @@
- name: peddy test_peddy
- command: nextflow run tests/modules/peddy -entry test_peddy -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/peddy -entry test_peddy -c ./tests/config/nextflow.config ./tests/modules/peddy/nextflow.config
tags:
- peddy
files:
diff --git a/tests/modules/phyloflash/main.nf b/tests/modules/phyloflash/main.nf
index 754d6747..412e0321 100644
--- a/tests/modules/phyloflash/main.nf
+++ b/tests/modules/phyloflash/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PHYLOFLASH } from '../../../modules/phyloflash/main.nf' addParams( options: [:] )
+include { PHYLOFLASH } from '../../../modules/phyloflash/main.nf'
process STUB_PHYLOFLASH_DATABASE {
output:
@@ -19,22 +19,22 @@ process STUB_PHYLOFLASH_DATABASE {
workflow test_phyloflash_single_end {
STUB_PHYLOFLASH_DATABASE ()
-
- input = [
+
+ input = [
[ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
- PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db, STUB_PHYLOFLASH_DATABASE.out.univec_db )
+ PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db, STUB_PHYLOFLASH_DATABASE.out.univec_db )
}
workflow test_phyloflash_paired_end {
STUB_PHYLOFLASH_DATABASE ()
- input = [
+ input = [
[ id:'test', single_end:false ], // meta map
- [
+ [
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
]
diff --git a/tests/modules/phyloflash/nextflow.config b/tests/modules/phyloflash/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/phyloflash/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/phyloflash/test.yml b/tests/modules/phyloflash/test.yml
index 0cba41c5..81eac2f2 100644
--- a/tests/modules/phyloflash/test.yml
+++ b/tests/modules/phyloflash/test.yml
@@ -1,5 +1,5 @@
- name: phyloflash single-end
- command: nextflow run ./tests/modules/phyloflash -entry test_phyloflash_single_end -c tests/config/nextflow.config -stub-run
+ command: nextflow run ./tests/modules/phyloflash -entry test_phyloflash_single_end -c ./tests/config/nextflow.config -c ./tests/modules/phyloflash/nextflow.config -stub-run
tags:
- phyloflash
files:
@@ -7,7 +7,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: phyloflash paired-end
- command: nextflow run ./tests/modules/phyloflash -entry test_phyloflash_paired_end -c tests/config/nextflow.config -stub-run
+ command: nextflow run ./tests/modules/phyloflash -entry test_phyloflash_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/phyloflash/nextflow.config -stub-run
tags:
- phyloflash
files:
diff --git a/tests/modules/picard/collecthsmetrics/main.nf b/tests/modules/picard/collecthsmetrics/main.nf
index 24b031fc..2e8727b5 100644
--- a/tests/modules/picard/collecthsmetrics/main.nf
+++ b/tests/modules/picard/collecthsmetrics/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsmetrics/main.nf' addParams( options: [:] )
+include { PICARD_COLLECTHSMETRICS } from '../../../../modules/picard/collecthsmetrics/main.nf'
workflow test_picard_collecthsmetrics {
diff --git a/tests/modules/picard/collecthsmetrics/nextflow.config b/tests/modules/picard/collecthsmetrics/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/picard/collecthsmetrics/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/picard/collecthsmetrics/test.yml b/tests/modules/picard/collecthsmetrics/test.yml
index 8c610abd..9232d508 100644
--- a/tests/modules/picard/collecthsmetrics/test.yml
+++ b/tests/modules/picard/collecthsmetrics/test.yml
@@ -1,5 +1,5 @@
- name: picard collecthsmetrics test_picard_collecthsmetrics
- command: nextflow run tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
tags:
- picard
- picard/collecthsmetrics
diff --git a/tests/modules/picard/collectmultiplemetrics/main.nf b/tests/modules/picard/collectmultiplemetrics/main.nf
index 73ac0013..453ecc91 100644
--- a/tests/modules/picard/collectmultiplemetrics/main.nf
+++ b/tests/modules/picard/collectmultiplemetrics/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
workflow test_picard_collectmultiplemetrics {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/picard/collectmultiplemetrics/nextflow.config b/tests/modules/picard/collectmultiplemetrics/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/picard/collectmultiplemetrics/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/picard/collectmultiplemetrics/test.yml
index fc4d0347..8fecca73 100644
--- a/tests/modules/picard/collectmultiplemetrics/test.yml
+++ b/tests/modules/picard/collectmultiplemetrics/test.yml
@@ -1,5 +1,5 @@
- name: picard collectmultiplemetrics
- command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
tags:
- picard
- picard/collectmultiplemetrics
diff --git a/tests/modules/picard/collectwgsmetrics/main.nf b/tests/modules/picard/collectwgsmetrics/main.nf
index 5bdf17ab..1d75a2bd 100644
--- a/tests/modules/picard/collectwgsmetrics/main.nf
+++ b/tests/modules/picard/collectwgsmetrics/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgsmetrics/main.nf' addParams( options: [:] )
+include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgsmetrics/main.nf'
workflow test_picard_collectwgsmetrics {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/picard/collectwgsmetrics/nextflow.config b/tests/modules/picard/collectwgsmetrics/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/picard/collectwgsmetrics/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/picard/collectwgsmetrics/test.yml
index 62e87e65..2daef406 100644
--- a/tests/modules/picard/collectwgsmetrics/test.yml
+++ b/tests/modules/picard/collectwgsmetrics/test.yml
@@ -1,5 +1,5 @@
- name: picard collectwgsmetrics test_picard_collectwgsmetrics
- command: nextflow run tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectwgsmetrics/nextflow.config
tags:
- picard/collectwgsmetrics
- picard
diff --git a/tests/modules/picard/filtersamreads/main.nf b/tests/modules/picard/filtersamreads/main.nf
index a03471dd..847bee57 100644
--- a/tests/modules/picard/filtersamreads/main.nf
+++ b/tests/modules/picard/filtersamreads/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' addParams( options: [suffix:'.sorted'] )
-include { PICARD_FILTERSAMREADS } from '../../../../modules/picard/filtersamreads/main.nf' addParams( options: [suffix:'.filtered'] )
+include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf'
+include { PICARD_FILTERSAMREADS } from '../../../../modules/picard/filtersamreads/main.nf'
workflow test_picard_filtersamreads {
diff --git a/tests/modules/picard/filtersamreads/nextflow.config b/tests/modules/picard/filtersamreads/nextflow.config
new file mode 100644
index 00000000..e9ce4914
--- /dev/null
+++ b/tests/modules/picard/filtersamreads/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PICARD_SORTSAM {
+ ext.suffix = '.sorted'
+ }
+
+ withName: PICARD_FILTERSAMREADS {
+ ext.suffix = '.filtered'
+ }
+
+}
diff --git a/tests/modules/picard/filtersamreads/test.yml b/tests/modules/picard/filtersamreads/test.yml
index e8e73ed0..a0ab712b 100644
--- a/tests/modules/picard/filtersamreads/test.yml
+++ b/tests/modules/picard/filtersamreads/test.yml
@@ -1,5 +1,5 @@
- name: picard filtersamreads
- command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads -c ./tests/config/nextflow.config -c ./tests/modules/picard/filtersamreads/nextflow.config
tags:
- picard
- picard/filtersamreads
@@ -9,7 +9,7 @@
- name: picard filtersamreads readlist
- command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/picard/filtersamreads/nextflow.config
tags:
- picard
- picard/filtersamreads
diff --git a/tests/modules/picard/markduplicates/main.nf b/tests/modules/picard/markduplicates/main.nf
index 7c9c63cd..12f3ac26 100644
--- a/tests/modules/picard/markduplicates/main.nf
+++ b/tests/modules/picard/markduplicates/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
-include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : 'ASSUME_SORT_ORDER=queryname' ] )
+include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf'
+include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf'
workflow test_picard_markduplicates_sorted_bam {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/picard/markduplicates/nextflow.config b/tests/modules/picard/markduplicates/nextflow.config
new file mode 100644
index 00000000..9178c5b1
--- /dev/null
+++ b/tests/modules/picard/markduplicates/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PICARD_MARKDUPLICATES_UNSORTED {
+ ext.args = 'ASSUME_SORT_ORDER=queryname'
+ }
+
+}
diff --git a/tests/modules/picard/markduplicates/test.yml b/tests/modules/picard/markduplicates/test.yml
index 4c314814..beb54009 100644
--- a/tests/modules/picard/markduplicates/test.yml
+++ b/tests/modules/picard/markduplicates/test.yml
@@ -1,5 +1,5 @@
- name: picard markduplicates sorted bam
- command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/picard/markduplicates/nextflow.config
tags:
- picard
- picard/markduplicates
@@ -9,7 +9,7 @@
- "1.0 97 97"
- path: ./output/picard/test.bam
- name: picard markduplicates unsorted bam
- command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/picard/markduplicates/nextflow.config
tags:
- picard
- picard/markduplicates
diff --git a/tests/modules/picard/mergesamfiles/main.nf b/tests/modules/picard/mergesamfiles/main.nf
index 5ddc849f..51c070b6 100644
--- a/tests/modules/picard/mergesamfiles/main.nf
+++ b/tests/modules/picard/mergesamfiles/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PICARD_MERGESAMFILES } from '../../../../modules/picard/mergesamfiles/main.nf' addParams( options: [:] )
+include { PICARD_MERGESAMFILES } from '../../../../modules/picard/mergesamfiles/main.nf'
workflow test_picard_mergesamfiles {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/picard/mergesamfiles/nextflow.config b/tests/modules/picard/mergesamfiles/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/picard/mergesamfiles/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/picard/mergesamfiles/test.yml b/tests/modules/picard/mergesamfiles/test.yml
index a331c96f..1cf59cb7 100644
--- a/tests/modules/picard/mergesamfiles/test.yml
+++ b/tests/modules/picard/mergesamfiles/test.yml
@@ -1,5 +1,5 @@
- name: picard mergesamfiles
- command: nextflow run ./tests/modules/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/mergesamfiles -entry test_picard_mergesamfiles -c ./tests/config/nextflow.config -c ./tests/modules/picard/mergesamfiles/nextflow.config
tags:
- picard
- picard/mergesamfiles
diff --git a/tests/modules/picard/sortsam/main.nf b/tests/modules/picard/sortsam/main.nf
index 0130fad6..1516682c 100644
--- a/tests/modules/picard/sortsam/main.nf
+++ b/tests/modules/picard/sortsam/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf' addParams( options: [suffix:'.sorted'] )
+include { PICARD_SORTSAM } from '../../../../modules/picard/sortsam/main.nf'
workflow test_picard_sortsam {
diff --git a/tests/modules/picard/sortsam/nextflow.config b/tests/modules/picard/sortsam/nextflow.config
new file mode 100644
index 00000000..2c290cbe
--- /dev/null
+++ b/tests/modules/picard/sortsam/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PICARD_SORTSAM {
+ ext.suffix = '.sorted'
+ }
+
+}
diff --git a/tests/modules/picard/sortsam/test.yml b/tests/modules/picard/sortsam/test.yml
index 4443228e..61521850 100644
--- a/tests/modules/picard/sortsam/test.yml
+++ b/tests/modules/picard/sortsam/test.yml
@@ -1,5 +1,5 @@
- name: picard sortsam
- command: nextflow run ./tests/modules/picard/sortsam -entry test_picard_sortsam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/picard/sortsam -entry test_picard_sortsam -c ./tests/config/nextflow.config -c ./tests/modules/picard/sortsam/nextflow.config
tags:
- picard
- picard/sortsam
diff --git a/tests/modules/pirate/main.nf b/tests/modules/pirate/main.nf
index 5957b1e6..05e5bdd8 100644
--- a/tests/modules/pirate/main.nf
+++ b/tests/modules/pirate/main.nf
@@ -2,15 +2,22 @@
nextflow.enable.dsl = 2
-include { PIRATE } from '../../../modules/pirate/main.nf' addParams( options: [:] )
+include { PIRATE } from '../../../modules/pirate/main.nf'
workflow test_pirate {
-
- input = [ [ id:'test', single_end:false ], // meta map
- [ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
+
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
+ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
+ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
+ ]
]
+ // [ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
+ // file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
+ // file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
+ // ]
PIRATE ( input )
}
diff --git a/tests/modules/pirate/nextflow.config b/tests/modules/pirate/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pirate/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pirate/test.yml b/tests/modules/pirate/test.yml
index d8c4d0c4..b8d36b95 100644
--- a/tests/modules/pirate/test.yml
+++ b/tests/modules/pirate/test.yml
@@ -1,5 +1,5 @@
- name: pirate test_pirate
- command: nextflow run tests/modules/pirate -entry test_pirate -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pirate -entry test_pirate -c ./tests/config/nextflow.config -c ./tests/modules/pirate/nextflow.config
tags:
- pirate
files:
diff --git a/tests/modules/plasmidid/main.nf b/tests/modules/plasmidid/main.nf
index 1dd57daf..52d25a91 100644
--- a/tests/modules/plasmidid/main.nf
+++ b/tests/modules/plasmidid/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PLASMIDID } from '../../../modules/plasmidid/main.nf' addParams ( options: ['args' : '-k 0.8'] )
+include { PLASMIDID } from '../../../modules/plasmidid/main.nf'
workflow test_plasmidid {
diff --git a/tests/modules/plasmidid/nextflow.config b/tests/modules/plasmidid/nextflow.config
new file mode 100644
index 00000000..2090bfae
--- /dev/null
+++ b/tests/modules/plasmidid/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PLASMIDID {
+ ext.args = '-k 0.8'
+ }
+
+}
diff --git a/tests/modules/plasmidid/test.yml b/tests/modules/plasmidid/test.yml
index 838af394..cd0528cb 100644
--- a/tests/modules/plasmidid/test.yml
+++ b/tests/modules/plasmidid/test.yml
@@ -1,5 +1,5 @@
- name: plasmidid
- command: nextflow run ./tests/modules/plasmidid -entry test_plasmidid -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/plasmidid -entry test_plasmidid -c ./tests/config/nextflow.config -c ./tests/modules/plasmidid/nextflow.config
tags:
- plasmidid
files:
diff --git a/tests/modules/plink/extract/main.nf b/tests/modules/plink/extract/main.nf
index e031a7b7..6beb0469 100644
--- a/tests/modules/plink/extract/main.nf
+++ b/tests/modules/plink/extract/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' addParams ( options: [args:'--make-bed --set-missing-var-ids @:#:\\$1:\\$2'])
-include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf' addParams( options: [suffix:'.extract'] )
+include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf'
+include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf'
workflow test_plink_extract {
diff --git a/tests/modules/plink/extract/nextflow.config b/tests/modules/plink/extract/nextflow.config
new file mode 100644
index 00000000..12668b01
--- /dev/null
+++ b/tests/modules/plink/extract/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PLINK_VCF {
+ ext.args = '--make-bed --set-missing-var-ids @:#:\\$1:\\$2'
+ }
+
+ withName: PLINK_EXTRACT {
+ ext.suffix = '.extract'
+ }
+
+}
diff --git a/tests/modules/plink/extract/test.yml b/tests/modules/plink/extract/test.yml
index 40569d9d..87cf82cc 100644
--- a/tests/modules/plink/extract/test.yml
+++ b/tests/modules/plink/extract/test.yml
@@ -1,5 +1,5 @@
- name: plink extract test_plink_extract
- command: nextflow run tests/modules/plink/extract -entry test_plink_extract -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/plink/extract -entry test_plink_extract -c ./tests/config/nextflow.config -c ./tests/modules/plink/extract/nextflow.config
tags:
- plink
- plink/extract
diff --git a/tests/modules/plink/vcf/main.nf b/tests/modules/plink/vcf/main.nf
index 096bacdd..4dac8978 100644
--- a/tests/modules/plink/vcf/main.nf
+++ b/tests/modules/plink/vcf/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' addParams( options: ['args':" --make-bed --biallelic-only strict --vcf-half-call missing --double-id --recode ped --id-delim \'=\' --allow-extra-chr"])
+include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf'
workflow test_plink_vcf {
diff --git a/tests/modules/plink/vcf/nextflow.config b/tests/modules/plink/vcf/nextflow.config
new file mode 100644
index 00000000..f0b72c8d
--- /dev/null
+++ b/tests/modules/plink/vcf/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PLINK_VCF {
+ ext.args = ' --make-bed --biallelic-only strict --vcf-half-call missing --double-id --recode ped --id-delim \'=\' --allow-extra-chr'
+ }
+
+}
diff --git a/tests/modules/plink/vcf/test.yml b/tests/modules/plink/vcf/test.yml
index bfd54386..9042d14a 100644
--- a/tests/modules/plink/vcf/test.yml
+++ b/tests/modules/plink/vcf/test.yml
@@ -1,5 +1,5 @@
- name: plink vcf test_plink_vcf
- command: nextflow run tests/modules/plink/vcf -entry test_plink_vcf -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/plink/vcf -entry test_plink_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink/vcf/nextflow.config
tags:
- plink
- plink/vcf
diff --git a/tests/modules/plink2/vcf/main.nf b/tests/modules/plink2/vcf/main.nf
index 409e7995..08d7dc61 100644
--- a/tests/modules/plink2/vcf/main.nf
+++ b/tests/modules/plink2/vcf/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf' addParams( options: [args:'--allow-extra-chr'] )
+include { PLINK2_VCF } from '../../../../modules/plink2/vcf/main.nf'
workflow test_plink2_vcf {
diff --git a/tests/modules/plink2/vcf/nextflow.config b/tests/modules/plink2/vcf/nextflow.config
new file mode 100644
index 00000000..7f7e5e77
--- /dev/null
+++ b/tests/modules/plink2/vcf/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PLINK2_VCF {
+ ext.args = '--allow-extra-chr'
+ }
+
+}
diff --git a/tests/modules/plink2/vcf/test.yml b/tests/modules/plink2/vcf/test.yml
index 3f0cddc6..52f58a42 100644
--- a/tests/modules/plink2/vcf/test.yml
+++ b/tests/modules/plink2/vcf/test.yml
@@ -1,5 +1,5 @@
- name: plink2 vcf test_plink2_vcf
- command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink2/vcf/nextflow.config
tags:
- plink2/vcf
- plink2
diff --git a/tests/modules/pmdtools/filter/main.nf b/tests/modules/pmdtools/filter/main.nf
index c4832bbb..f1b2b4d3 100644
--- a/tests/modules/pmdtools/filter/main.nf
+++ b/tests/modules/pmdtools/filter/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PMDTOOLS_FILTER } from '../../../../modules/pmdtools/filter/main.nf' addParams( options: [:] )
+include { PMDTOOLS_FILTER } from '../../../../modules/pmdtools/filter/main.nf'
workflow test_pmdtools_filter {
diff --git a/tests/modules/pmdtools/filter/nextflow.config b/tests/modules/pmdtools/filter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pmdtools/filter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pmdtools/filter/test.yml b/tests/modules/pmdtools/filter/test.yml
index 9171b02e..a7ebefbe 100644
--- a/tests/modules/pmdtools/filter/test.yml
+++ b/tests/modules/pmdtools/filter/test.yml
@@ -1,5 +1,5 @@
- name: pmdtools filter
- command: nextflow run ./tests/modules/pmdtools/filter -entry test_pmdtools_filter -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pmdtools/filter -entry test_pmdtools_filter -c ./tests/config/nextflow.config -c ./tests/modules/pmdtools/filter/nextflow.config
tags:
- pmdtools
- pmdtools/filter
diff --git a/tests/modules/porechop/main.nf b/tests/modules/porechop/main.nf
index b6d7bafa..f20b7a6e 100644
--- a/tests/modules/porechop/main.nf
+++ b/tests/modules/porechop/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PORECHOP } from '../../../modules/porechop/main.nf' addParams( options: [args: '', suffix: '_porechop'] )
+include { PORECHOP } from '../../../modules/porechop/main.nf'
workflow test_porechop {
diff --git a/tests/modules/porechop/nextflow.config b/tests/modules/porechop/nextflow.config
new file mode 100644
index 00000000..3a0536b0
--- /dev/null
+++ b/tests/modules/porechop/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PORECHOP {
+ ext.args = ''
+ ext.suffix = '_porechop'
+ }
+
+}
diff --git a/tests/modules/porechop/test.yml b/tests/modules/porechop/test.yml
index b37a7ec4..8790ab87 100644
--- a/tests/modules/porechop/test.yml
+++ b/tests/modules/porechop/test.yml
@@ -1,5 +1,5 @@
- name: porechop test_porechop
- command: nextflow run tests/modules/porechop -entry test_porechop -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/porechop -entry test_porechop -c ./tests/config/nextflow.config -c ./tests/modules/porechop/nextflow.config
tags:
- porechop
files:
diff --git a/tests/modules/preseq/lcextrap/main.nf b/tests/modules/preseq/lcextrap/main.nf
index 390039bd..4bbbd146 100644
--- a/tests/modules/preseq/lcextrap/main.nf
+++ b/tests/modules/preseq/lcextrap/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PRESEQ_LCEXTRAP } from '../../../../modules/preseq/lcextrap/main.nf' addParams( options: [:] )
+include { PRESEQ_LCEXTRAP } from '../../../../modules/preseq/lcextrap/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/preseq/lcextrap/nextflow.config b/tests/modules/preseq/lcextrap/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/preseq/lcextrap/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/preseq/lcextrap/test.yml b/tests/modules/preseq/lcextrap/test.yml
index 4472a485..ecd1d046 100644
--- a/tests/modules/preseq/lcextrap/test.yml
+++ b/tests/modules/preseq/lcextrap/test.yml
@@ -1,5 +1,5 @@
- name: preseq lcextrap single-end
- command: nextflow run ./tests/modules/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/preseq/lcextrap -entry test_preseq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/lcextrap/nextflow.config
tags:
- preseq
- preseq/lcextrap
@@ -9,7 +9,7 @@
- path: output/preseq/test.command.log
- name: preseq lcextrap paired-end
- command: nextflow run ./tests/modules/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/preseq/lcextrap -entry test_preseq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/lcextrap/nextflow.config
tags:
- preseq
- preseq/lcextrap
diff --git a/tests/modules/prodigal/main.nf b/tests/modules/prodigal/main.nf
index 414585a1..6e282015 100644
--- a/tests/modules/prodigal/main.nf
+++ b/tests/modules/prodigal/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PRODIGAL } from '../../../modules/prodigal/main.nf' addParams( options: [:] )
+include { PRODIGAL } from '../../../modules/prodigal/main.nf'
workflow test_prodigal {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/prodigal/nextflow.config b/tests/modules/prodigal/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/prodigal/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/prodigal/test.yml b/tests/modules/prodigal/test.yml
index 93caa998..7f0ab88c 100644
--- a/tests/modules/prodigal/test.yml
+++ b/tests/modules/prodigal/test.yml
@@ -1,5 +1,5 @@
- name: prodigal test_prodigal
- command: nextflow run tests/modules/prodigal -entry test_prodigal -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/prodigal -entry test_prodigal -c ./tests/config/nextflow.config -c ./tests/modules/prodigal/nextflow.config
tags:
- prodigal
files:
diff --git a/tests/modules/prokka/main.nf b/tests/modules/prokka/main.nf
index e35cb1d9..97e94ca8 100644
--- a/tests/modules/prokka/main.nf
+++ b/tests/modules/prokka/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PROKKA } from '../../../modules/prokka/main.nf' addParams( options: [:] )
+include { PROKKA } from '../../../modules/prokka/main.nf'
workflow test_prokka {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/prokka/nextflow.config b/tests/modules/prokka/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/prokka/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/prokka/test.yml b/tests/modules/prokka/test.yml
index 2823353c..92f813a7 100644
--- a/tests/modules/prokka/test.yml
+++ b/tests/modules/prokka/test.yml
@@ -1,5 +1,5 @@
- name: prokka
- command: nextflow run ./tests/modules/prokka -entry test_prokka -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/prokka -entry test_prokka -c ./tests/config/nextflow.config -c ./tests/modules/prokka/nextflow.config
tags:
- prokka
files:
diff --git a/tests/modules/pycoqc/main.nf b/tests/modules/pycoqc/main.nf
index ab65dadc..c8a8ee2c 100644
--- a/tests/modules/pycoqc/main.nf
+++ b/tests/modules/pycoqc/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PYCOQC } from '../../../modules/pycoqc/main.nf' addParams ( options: ['args' : '--min_pass_qual 0'] )
+include { PYCOQC } from '../../../modules/pycoqc/main.nf'
workflow test_pycoqc {
diff --git a/tests/modules/pycoqc/nextflow.config b/tests/modules/pycoqc/nextflow.config
new file mode 100644
index 00000000..d532f8f7
--- /dev/null
+++ b/tests/modules/pycoqc/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: PYCOQC {
+ ext.args = '--min_pass_qual 0'
+ }
+
+}
diff --git a/tests/modules/pycoqc/test.yml b/tests/modules/pycoqc/test.yml
index 052e3e1a..becd911b 100644
--- a/tests/modules/pycoqc/test.yml
+++ b/tests/modules/pycoqc/test.yml
@@ -1,5 +1,5 @@
- name: pycoqc
- command: nextflow run ./tests/modules/pycoqc -entry test_pycoqc -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pycoqc -entry test_pycoqc -c ./tests/config/nextflow.config -c ./tests/modules/pycoqc/nextflow.config
tags:
- pycoqc
files:
diff --git a/tests/modules/pydamage/analyze/main.nf b/tests/modules/pydamage/analyze/main.nf
index ddf0b27a..920a4201 100644
--- a/tests/modules/pydamage/analyze/main.nf
+++ b/tests/modules/pydamage/analyze/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf' addParams( options: [:] )
+include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf'
workflow test_pydamage {
diff --git a/tests/modules/pydamage/analyze/nextflow.config b/tests/modules/pydamage/analyze/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pydamage/analyze/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pydamage/analyze/test.yml b/tests/modules/pydamage/analyze/test.yml
index 157e947f..9d22f20e 100644
--- a/tests/modules/pydamage/analyze/test.yml
+++ b/tests/modules/pydamage/analyze/test.yml
@@ -1,5 +1,5 @@
- name: pydamage analyze test workflow
- command: nextflow run tests/modules/pydamage/analyze -entry test_pydamage -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pydamage/analyze -entry test_pydamage -c ./tests/config/nextflow.config -c ./tests/modules/pydamage/analyze/nextflow.config
tags:
- pydamage
- pydamage/analyze
diff --git a/tests/modules/pydamage/filter/main.nf b/tests/modules/pydamage/filter/main.nf
index 03e90408..dac03e78 100644
--- a/tests/modules/pydamage/filter/main.nf
+++ b/tests/modules/pydamage/filter/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf' addParams( options: [:] )
-include { PYDAMAGE_FILTER } from '../../../../modules/pydamage/filter/main.nf' addParams( options: [:] )
+include { PYDAMAGE_ANALYZE } from '../../../../modules/pydamage/analyze/main.nf'
+include { PYDAMAGE_FILTER } from '../../../../modules/pydamage/filter/main.nf'
workflow test_pydamage {
diff --git a/tests/modules/pydamage/filter/nextflow.config b/tests/modules/pydamage/filter/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/pydamage/filter/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/pydamage/filter/test.yml b/tests/modules/pydamage/filter/test.yml
index 248be44b..b6738e3d 100644
--- a/tests/modules/pydamage/filter/test.yml
+++ b/tests/modules/pydamage/filter/test.yml
@@ -1,5 +1,5 @@
- name: pydamage filter test workflow
- command: nextflow run tests/modules/pydamage/filter -entry test_pydamage -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/pydamage/filter -entry test_pydamage -c ./tests/config/nextflow.config -c ./tests/modules/pydamage/filter/nextflow.config
tags:
- pydamage
- pydamage/filter
@@ -7,4 +7,4 @@
- path: output/pydamage/pydamage_results/pydamage_filtered_results.csv
md5sum: 9f297233cf4932d7d7e52cc72d4727dc
- path: output/pydamage/pydamage_results/pydamage_results.csv
- md5sum: 6847e0d5aa6dba85bbd2dd509772b7a0
+ md5sum: 37ee6b4dee6890fd2ec8550337f21ac9
diff --git a/tests/modules/qcat/main.nf b/tests/modules/qcat/main.nf
index 72c87e37..8a5cdd6d 100644
--- a/tests/modules/qcat/main.nf
+++ b/tests/modules/qcat/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { QCAT } from '../../../modules/qcat/main.nf' addParams( options: [:] )
+include { QCAT } from '../../../modules/qcat/main.nf'
workflow test_qcat {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/qcat/nextflow.config b/tests/modules/qcat/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/qcat/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/qcat/test.yml b/tests/modules/qcat/test.yml
index 5c43841b..47ece983 100644
--- a/tests/modules/qcat/test.yml
+++ b/tests/modules/qcat/test.yml
@@ -1,5 +1,5 @@
- name: qcat
- command: nextflow run ./tests/modules/qcat -entry test_qcat -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/qcat -entry test_qcat -c ./tests/config/nextflow.config -c ./tests/modules/qcat/nextflow.config
tags:
- qcat
files:
diff --git a/tests/modules/qualimap/bamqc/main.nf b/tests/modules/qualimap/bamqc/main.nf
index 803d0220..a17efd59 100644
--- a/tests/modules/qualimap/bamqc/main.nf
+++ b/tests/modules/qualimap/bamqc/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { QUALIMAP_BAMQC } from '../../../../modules/qualimap/bamqc/main.nf' addParams( options: [:] )
+include { QUALIMAP_BAMQC } from '../../../../modules/qualimap/bamqc/main.nf'
workflow test_qualimap_bamqc {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/qualimap/bamqc/nextflow.config b/tests/modules/qualimap/bamqc/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/qualimap/bamqc/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/qualimap/bamqc/test.yml b/tests/modules/qualimap/bamqc/test.yml
index 7d746a51..41c4199e 100644
--- a/tests/modules/qualimap/bamqc/test.yml
+++ b/tests/modules/qualimap/bamqc/test.yml
@@ -1,5 +1,5 @@
- name: qualimap bamqc test workflow
- command: nextflow run ./tests/modules/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/qualimap/bamqc -entry test_qualimap_bamqc -c ./tests/config/nextflow.config -c ./tests/modules/qualimap/bamqc/nextflow.config
tags:
- qualimap
- qualimap/bamqc
diff --git a/tests/modules/quast/main.nf b/tests/modules/quast/main.nf
index d263470c..c879a8a9 100644
--- a/tests/modules/quast/main.nf
+++ b/tests/modules/quast/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { QUAST } from '../../../modules/quast/main.nf' addParams(options: [:])
+include { QUAST } from '../../../modules/quast/main.nf'
workflow test_quast_ref {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/quast/nextflow.config b/tests/modules/quast/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/quast/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/quast/test.yml b/tests/modules/quast/test.yml
index 6e1f991f..166cd896 100644
--- a/tests/modules/quast/test.yml
+++ b/tests/modules/quast/test.yml
@@ -1,5 +1,5 @@
- name: quast with reference
- command: nextflow run ./tests/modules/quast -entry test_quast_ref -c ./tests/config/nextflow.config
+ command: nextflow run ./tests/modules/quast -entry test_quast_ref -c ./tests/config/nextflow.config -c ./tests/modules/quast/nextflow.config
tags:
- quast
files:
@@ -82,7 +82,7 @@
- path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
- name: quast without reference
- command: nextflow run ./tests/modules/quast -entry test_quast_noref -c ./tests/config/nextflow.config
+ command: nextflow run ./tests/modules/quast -entry test_quast_noref -c ./tests/config/nextflow.config -c ./tests/modules/quast/nextflow.config
tags:
- quast
files:
diff --git a/tests/modules/racon/main.nf b/tests/modules/racon/main.nf
index b6b864e1..507d8d8d 100644
--- a/tests/modules/racon/main.nf
+++ b/tests/modules/racon/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RACON } from '../../../modules/racon/main.nf' addParams( options: [:] )
+include { RACON } from '../../../modules/racon/main.nf'
workflow test_racon {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/racon/nextflow.config b/tests/modules/racon/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/racon/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/racon/test.yml b/tests/modules/racon/test.yml
index dc8e57dc..0250fa36 100644
--- a/tests/modules/racon/test.yml
+++ b/tests/modules/racon/test.yml
@@ -1,5 +1,5 @@
- name: racon test_racon
- command: nextflow run tests/modules/racon -entry test_racon -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/racon -entry test_racon -c ./tests/config/nextflow.config -c ./tests/modules/racon/nextflow.config
tags:
- racon
files:
diff --git a/tests/modules/rapidnj/main.nf b/tests/modules/rapidnj/main.nf
index e23fa46f..66d19c3c 100644
--- a/tests/modules/rapidnj/main.nf
+++ b/tests/modules/rapidnj/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RAPIDNJ } from '../../../modules/rapidnj/main.nf' addParams( options: [:] )
+include { RAPIDNJ } from '../../../modules/rapidnj/main.nf'
workflow test_rapidnj {
diff --git a/tests/modules/rapidnj/nextflow.config b/tests/modules/rapidnj/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rapidnj/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rapidnj/test.yml b/tests/modules/rapidnj/test.yml
index 0b7ecff5..21f6ead9 100644
--- a/tests/modules/rapidnj/test.yml
+++ b/tests/modules/rapidnj/test.yml
@@ -1,5 +1,5 @@
- name: rapidnj
- command: nextflow run ./tests/modules/rapidnj -entry test_rapidnj -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rapidnj -entry test_rapidnj -c ./tests/config/nextflow.config -c ./tests/modules/rapidnj/nextflow.config
tags:
- rapidnj
files:
diff --git a/tests/modules/rasusa/main.nf b/tests/modules/rasusa/main.nf
index 9cc139ad..8a11627c 100644
--- a/tests/modules/rasusa/main.nf
+++ b/tests/modules/rasusa/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RASUSA } from '../../../modules/rasusa/main.nf' addParams( options: ['suffix':'_100X'])
+include { RASUSA } from '../../../modules/rasusa/main.nf'
workflow test_rasusa {
input = [ [ id:'test', single_end:false], // meta map
diff --git a/tests/modules/rasusa/nextflow.config b/tests/modules/rasusa/nextflow.config
new file mode 100644
index 00000000..fea844ae
--- /dev/null
+++ b/tests/modules/rasusa/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: RASUSA {
+ ext.suffix = '_100X'
+ }
+
+}
diff --git a/tests/modules/rasusa/test.yml b/tests/modules/rasusa/test.yml
index bb30c99e..41c56b67 100644
--- a/tests/modules/rasusa/test.yml
+++ b/tests/modules/rasusa/test.yml
@@ -1,5 +1,5 @@
- name: rasusa test_rasusa
- command: nextflow run tests/modules/rasusa -entry test_rasusa -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rasusa -entry test_rasusa -c ./tests/config/nextflow.config -c ./tests/modules/rasusa/nextflow.config
tags:
- rasusa
files:
diff --git a/tests/modules/raxmlng/main.nf b/tests/modules/raxmlng/main.nf
index 2cac6b31..5fad6953 100644
--- a/tests/modules/raxmlng/main.nf
+++ b/tests/modules/raxmlng/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../modules/raxmlng/main.nf' addParams( options: [args:'--model GTR+G'] )
-include { RAXMLNG as RAXMLNG_BOOTSTRAP } from '../../../modules/raxmlng/main.nf' addParams( options: [args:'--all --model GTR+G --bs-trees 1000'] )
+include { RAXMLNG as RAXMLNG_NO_BOOTSTRAP } from '../../../modules/raxmlng/main.nf'
+include { RAXMLNG as RAXMLNG_BOOTSTRAP } from '../../../modules/raxmlng/main.nf'
//
// Test without bootstrapping
diff --git a/tests/modules/raxmlng/nextflow.config b/tests/modules/raxmlng/nextflow.config
new file mode 100644
index 00000000..8c269a9b
--- /dev/null
+++ b/tests/modules/raxmlng/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: RAXMLNG_NO_BOOTSTRAP {
+ ext.args = '--model GTR+G'
+ }
+
+ withName: RAXMLNG_BOOTSTRAP {
+ ext.args = '--all --model GTR+G --bs-trees 1000'
+ }
+
+}
diff --git a/tests/modules/raxmlng/test.yml b/tests/modules/raxmlng/test.yml
index 950c48ad..735b6a74 100644
--- a/tests/modules/raxmlng/test.yml
+++ b/tests/modules/raxmlng/test.yml
@@ -1,5 +1,5 @@
- name: raxmlng no_bootstrap
- command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_no_bootstrap -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_no_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/raxmlng/nextflow.config
tags:
- raxmlng
files:
@@ -11,7 +11,7 @@
- 'sample4:0.111'
- name: raxmlng bootstrap
- command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_bootstrap -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/raxmlng/nextflow.config
tags:
- raxmlng
files:
diff --git a/tests/modules/rmarkdownnotebook/main.nf b/tests/modules/rmarkdownnotebook/main.nf
index e56d54ff..fdb7d3b9 100644
--- a/tests/modules/rmarkdownnotebook/main.nf
+++ b/tests/modules/rmarkdownnotebook/main.nf
@@ -2,12 +2,8 @@
nextflow.enable.dsl = 2
-include { RMARKDOWNNOTEBOOK } from '../../../modules/rmarkdownnotebook/main.nf' addParams(
- parametrize: false, options: [:]
-)
-include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/rmarkdownnotebook/main.nf' addParams(
- options: [:]
-)
+include { RMARKDOWNNOTEBOOK } from '../../../modules/rmarkdownnotebook/main.nf'
+include { RMARKDOWNNOTEBOOK as RMARKDOWNNOTEBOOK_PARAMETRIZE } from '../../../modules/rmarkdownnotebook/main.nf'
workflow test_rmarkdown {
diff --git a/tests/modules/rmarkdownnotebook/nextflow.config b/tests/modules/rmarkdownnotebook/nextflow.config
new file mode 100644
index 00000000..c99f5250
--- /dev/null
+++ b/tests/modules/rmarkdownnotebook/nextflow.config
@@ -0,0 +1,15 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: RMARKDOWNNOTEBOOK {
+ ext = ['parametrize': false]
+ }
+
+ // this should be the default options, but need to work around
+ // https://github.com/nextflow-io/nextflow/issues/2422
+ withName: RMARKDOWNNOTEBOOK_PARAMETRIZE {
+ ext = ['parametrize': true]
+ }
+
+}
diff --git a/tests/modules/rmarkdownnotebook/test.yml b/tests/modules/rmarkdownnotebook/test.yml
index bef6086a..3645514a 100644
--- a/tests/modules/rmarkdownnotebook/test.yml
+++ b/tests/modules/rmarkdownnotebook/test.yml
@@ -1,5 +1,5 @@
- name: rmarkdownnotebook test_rmarkdown
- command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rmarkdownnotebook -entry test_rmarkdown -c ./tests/config/nextflow.config -c ./tests/modules/rmarkdownnotebook/nextflow.config
tags:
- rmarkdownnotebook
files:
@@ -12,7 +12,7 @@
- "n_iter = 10"
- name: rmarkdownnotebook test_rmarkdown_parametrize
- command: nextflow run tests/modules/rmarkdownnotebook -entry test_rmarkdown_parametrize -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rmarkdownnotebook -entry test_rmarkdown_parametrize -c ./tests/config/nextflow.config -c ./tests/modules/rmarkdownnotebook/nextflow.config
tags:
- rmarkdownnotebook
files:
diff --git a/tests/modules/roary/main.nf b/tests/modules/roary/main.nf
index a4a96d6e..3fae516c 100644
--- a/tests/modules/roary/main.nf
+++ b/tests/modules/roary/main.nf
@@ -2,14 +2,17 @@
nextflow.enable.dsl = 2
-include { ROARY } from '../../../modules/roary/main.nf' addParams( options: [:] )
+include { ROARY } from '../../../modules/roary/main.nf'
workflow test_roary {
-
- input = [ [ id:'test', single_end:false ], // meta map
- [ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
- file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
+
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
+ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
+ file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
+ ]
]
ROARY ( input )
diff --git a/tests/modules/roary/nextflow.config b/tests/modules/roary/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/roary/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/roary/test.yml b/tests/modules/roary/test.yml
index c8e8c33d..981ab51c 100644
--- a/tests/modules/roary/test.yml
+++ b/tests/modules/roary/test.yml
@@ -1,5 +1,5 @@
- name: roary test_roary
- command: nextflow run tests/modules/roary -entry test_roary -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/roary -entry test_roary -c ./tests/config/nextflow.config -c ./tests/modules/roary/nextflow.config
tags:
- roary
files:
@@ -8,9 +8,9 @@
- path: output/roary/results/accessory.tab
contains: ['FT']
- path: output/roary/results/accessory_binary_genes.fa
- md5sum: 0baeea4947bf17a2bf29d43a44f0278f
+ md5sum: d4191cf748dd8016ad877857a034bef3
- path: output/roary/results/accessory_binary_genes.fa.newick
- md5sum: b1f8c76ab231bd38b850c1f8d3c1584b
+ md5sum: d4a2a64e781263ca1b9b3a4bc9d3a6ea
- path: output/roary/results/accessory_graph.dot
contains: ['/* list of nodes */']
- path: output/roary/results/blast_identity_frequency.Rtab
@@ -20,7 +20,7 @@
- path: output/roary/results/core_accessory.header.embl
contains: ['ID Genome standard; DNA; PRO; 1234 BP.']
- path: output/roary/results/core_accessory.tab
- contains: ['FT /taxa="GCF_000292685 GCF_000298385 GCF_002849995"']
+ contains: ['FT /taxa="test1 test2 test3"']
- path: output/roary/results/core_accessory_graph.dot
contains: ['/* list of nodes */']
- path: output/roary/results/gene_presence_absence.Rtab
diff --git a/tests/modules/rsem/calculateexpression/main.nf b/tests/modules/rsem/calculateexpression/main.nf
index e7de83a4..9d6d3c5c 100644
--- a/tests/modules/rsem/calculateexpression/main.nf
+++ b/tests/modules/rsem/calculateexpression/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [args: "--star"])
-include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf' addParams(options: [args: "--star --star-gzipped-read-file"])
+include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf'
+include { RSEM_CALCULATEEXPRESSION } from '../../../../modules/rsem/calculateexpression/main.nf'
workflow test_rsem_calculateexpression {
diff --git a/tests/modules/rsem/calculateexpression/nextflow.config b/tests/modules/rsem/calculateexpression/nextflow.config
new file mode 100644
index 00000000..b17a1cf2
--- /dev/null
+++ b/tests/modules/rsem/calculateexpression/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: RSEM_PREPAREREFERENCE {
+ ext.args = '--star'
+ }
+
+ withName: RSEM_CALCULATEEXPRESSION {
+ ext.args = '--star --star-gzipped-read-file'
+ }
+
+}
diff --git a/tests/modules/rsem/calculateexpression/test.yml b/tests/modules/rsem/calculateexpression/test.yml
index ac0866ea..f19c3398 100644
--- a/tests/modules/rsem/calculateexpression/test.yml
+++ b/tests/modules/rsem/calculateexpression/test.yml
@@ -1,55 +1,55 @@
- name: rsem calculateexpression test_rsem_calculateexpression
- command: nextflow run tests/modules/rsem/calculateexpression -entry test_rsem_calculateexpression -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rsem/calculateexpression -entry test_rsem_calculateexpression -c ./tests/config/nextflow.config -c ./tests/modules/rsem/calculateexpression/nextflow.config
tags:
- rsem
- rsem/calculateexpression
files:
- - path: output/index/rsem/Genome
+ - path: output/rsem/rsem/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/rsem/Log.out
- - path: output/index/rsem/SA
+ - path: output/rsem/rsem/Log.out
+ - path: output/rsem/rsem/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/rsem/SAindex
+ - path: output/rsem/rsem/SAindex
md5sum: fd05c149960e72642a8d7c860528ae81
- - path: output/index/rsem/chrLength.txt
+ - path: output/rsem/rsem/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/rsem/chrName.txt
+ - path: output/rsem/rsem/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/rsem/chrNameLength.txt
+ - path: output/rsem/rsem/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/rsem/chrStart.txt
+ - path: output/rsem/rsem/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/rsem/exonGeTrInfo.tab
+ - path: output/rsem/rsem/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/rsem/exonInfo.tab
+ - path: output/rsem/rsem/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/rsem/geneInfo.tab
+ - path: output/rsem/rsem/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/rsem/genome.chrlist
+ - path: output/rsem/rsem/genome.chrlist
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/rsem/genome.fasta
+ - path: output/rsem/rsem/genome.fasta
md5sum: f315020d899597c1b57e5fe9f60f4c3e
- - path: output/index/rsem/genome.grp
+ - path: output/rsem/rsem/genome.grp
md5sum: c2848a8b6d495956c11ec53efc1de67e
- - path: output/index/rsem/genome.idx.fa
+ - path: output/rsem/rsem/genome.idx.fa
md5sum: 050c521a2719c2ae48267c1e65218f29
- - path: output/index/rsem/genome.n2g.idx.fa
+ - path: output/rsem/rsem/genome.n2g.idx.fa
md5sum: 050c521a2719c2ae48267c1e65218f29
- - path: output/index/rsem/genome.seq
+ - path: output/rsem/rsem/genome.seq
md5sum: 94da0c6b88c33e63c9a052a11f4f57c1
- - path: output/index/rsem/genome.ti
+ - path: output/rsem/rsem/genome.ti
md5sum: c9e4ae8d4d13a504eec2acf1b8589a66
- - path: output/index/rsem/genome.transcripts.fa
+ - path: output/rsem/rsem/genome.transcripts.fa
md5sum: 050c521a2719c2ae48267c1e65218f29
- - path: output/index/rsem/genomeParameters.txt
+ - path: output/rsem/rsem/genomeParameters.txt
md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f
- - path: output/index/rsem/sjdbInfo.txt
+ - path: output/rsem/rsem/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/rsem/sjdbList.fromGTF.out.tab
+ - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/rsem/sjdbList.out.tab
+ - path: output/rsem/rsem/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/rsem/transcriptInfo.tab
+ - path: output/rsem/rsem/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/rsem/test.genes.results
md5sum: c7ec226f76736ea805771e73553ae359
diff --git a/tests/modules/rsem/preparereference/main.nf b/tests/modules/rsem/preparereference/main.nf
index 2d4a9053..8062737d 100644
--- a/tests/modules/rsem/preparereference/main.nf
+++ b/tests/modules/rsem/preparereference/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf' addParams(options: [publish_dir:'rsem'])
+include { RSEM_PREPAREREFERENCE } from '../../../../modules/rsem/preparereference/main.nf'
workflow test_rsem_preparereference {
diff --git a/tests/modules/rsem/preparereference/nextflow.config b/tests/modules/rsem/preparereference/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rsem/preparereference/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rsem/preparereference/test.yml b/tests/modules/rsem/preparereference/test.yml
index 734a92b2..1f058bea 100644
--- a/tests/modules/rsem/preparereference/test.yml
+++ b/tests/modules/rsem/preparereference/test.yml
@@ -1,5 +1,5 @@
- name: rsem preparereference test_rsem_preparereference
- command: nextflow run tests/modules/rsem/preparereference -entry test_rsem_preparereference -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rsem/preparereference -entry test_rsem_preparereference -c ./tests/config/nextflow.config -c ./tests/modules/rsem/preparereference/nextflow.config
tags:
- rsem
- rsem/preparereference
diff --git a/tests/modules/rseqc/bamstat/main.nf b/tests/modules/rseqc/bamstat/main.nf
index c13e7f97..4c53a1af 100644
--- a/tests/modules/rseqc/bamstat/main.nf
+++ b/tests/modules/rseqc/bamstat/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_BAMSTAT } from '../../../../modules/rseqc/bamstat/main.nf' addParams(options: [:])
+include { RSEQC_BAMSTAT } from '../../../../modules/rseqc/bamstat/main.nf'
workflow test_rseqc_bamstat {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/rseqc/bamstat/nextflow.config b/tests/modules/rseqc/bamstat/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/bamstat/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/bamstat/test.yml b/tests/modules/rseqc/bamstat/test.yml
index 75d62672..4cb35d0c 100644
--- a/tests/modules/rseqc/bamstat/test.yml
+++ b/tests/modules/rseqc/bamstat/test.yml
@@ -1,5 +1,5 @@
- name: rseqc bamstat test_rseqc_bamstat
- command: nextflow run tests/modules/rseqc/bamstat -entry test_rseqc_bamstat -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/bamstat -entry test_rseqc_bamstat -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/bamstat/nextflow.config
tags:
- rseqc
- rseqc/bamstat
diff --git a/tests/modules/rseqc/inferexperiment/main.nf b/tests/modules/rseqc/inferexperiment/main.nf
index ae8c53a9..6337063d 100644
--- a/tests/modules/rseqc/inferexperiment/main.nf
+++ b/tests/modules/rseqc/inferexperiment/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_INFEREXPERIMENT } from '../../../../modules/rseqc/inferexperiment/main.nf' addParams(options: [:])
+include { RSEQC_INFEREXPERIMENT } from '../../../../modules/rseqc/inferexperiment/main.nf'
workflow test_rseqc_inferexperiment {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/rseqc/inferexperiment/nextflow.config b/tests/modules/rseqc/inferexperiment/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/inferexperiment/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/inferexperiment/test.yml b/tests/modules/rseqc/inferexperiment/test.yml
index 59d6f3d5..554f8317 100644
--- a/tests/modules/rseqc/inferexperiment/test.yml
+++ b/tests/modules/rseqc/inferexperiment/test.yml
@@ -1,5 +1,5 @@
- name: rseqc inferexperiment test_rseqc_inferexperiment
- command: nextflow run tests/modules/rseqc/inferexperiment -entry test_rseqc_inferexperiment -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/inferexperiment -entry test_rseqc_inferexperiment -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/inferexperiment/nextflow.config
tags:
- rseqc
- rseqc/inferexperiment
diff --git a/tests/modules/rseqc/innerdistance/main.nf b/tests/modules/rseqc/innerdistance/main.nf
index 003e8a14..8cc0ec3e 100644
--- a/tests/modules/rseqc/innerdistance/main.nf
+++ b/tests/modules/rseqc/innerdistance/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_INNERDISTANCE } from '../../../../modules/rseqc/innerdistance/main.nf' addParams(options: [:])
+include { RSEQC_INNERDISTANCE } from '../../../../modules/rseqc/innerdistance/main.nf'
workflow test_rseqc_innerdistance {
input = [ [ id:'test', single_end: false ], // meta map
diff --git a/tests/modules/rseqc/innerdistance/nextflow.config b/tests/modules/rseqc/innerdistance/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/innerdistance/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/innerdistance/test.yml b/tests/modules/rseqc/innerdistance/test.yml
index b0ee0283..c0f480e9 100644
--- a/tests/modules/rseqc/innerdistance/test.yml
+++ b/tests/modules/rseqc/innerdistance/test.yml
@@ -1,5 +1,5 @@
- name: rseqc innerdistance test_rseqc_innerdistance
- command: nextflow run tests/modules/rseqc/innerdistance -entry test_rseqc_innerdistance -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/innerdistance -entry test_rseqc_innerdistance -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/innerdistance/nextflow.config
tags:
- rseqc
- rseqc/innerdistance
diff --git a/tests/modules/rseqc/junctionannotation/main.nf b/tests/modules/rseqc/junctionannotation/main.nf
index a6913850..303dcd85 100644
--- a/tests/modules/rseqc/junctionannotation/main.nf
+++ b/tests/modules/rseqc/junctionannotation/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_JUNCTIONANNOTATION } from '../../../../modules/rseqc/junctionannotation/main.nf' addParams(options: [:])
+include { RSEQC_JUNCTIONANNOTATION } from '../../../../modules/rseqc/junctionannotation/main.nf'
workflow test_rseqc_junctionannotation {
input = [
diff --git a/tests/modules/rseqc/junctionannotation/nextflow.config b/tests/modules/rseqc/junctionannotation/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/junctionannotation/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/junctionannotation/test.yml b/tests/modules/rseqc/junctionannotation/test.yml
index 39326f67..f2020b10 100644
--- a/tests/modules/rseqc/junctionannotation/test.yml
+++ b/tests/modules/rseqc/junctionannotation/test.yml
@@ -1,5 +1,5 @@
- name: rseqc junctionannotation test_rseqc_junctionannotation
- command: nextflow run tests/modules/rseqc/junctionannotation -entry test_rseqc_junctionannotation -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/junctionannotation -entry test_rseqc_junctionannotation -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/junctionannotation/nextflow.config
tags:
- rseqc
- rseqc/junctionannotation
diff --git a/tests/modules/rseqc/junctionsaturation/main.nf b/tests/modules/rseqc/junctionsaturation/main.nf
index 047fb372..eefbb492 100644
--- a/tests/modules/rseqc/junctionsaturation/main.nf
+++ b/tests/modules/rseqc/junctionsaturation/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_JUNCTIONSATURATION } from '../../../../modules/rseqc/junctionsaturation/main.nf' addParams(options: [:])
+include { RSEQC_JUNCTIONSATURATION } from '../../../../modules/rseqc/junctionsaturation/main.nf'
workflow test_rseqc_junctionsaturation {
input = [
diff --git a/tests/modules/rseqc/junctionsaturation/nextflow.config b/tests/modules/rseqc/junctionsaturation/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/junctionsaturation/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/junctionsaturation/test.yml b/tests/modules/rseqc/junctionsaturation/test.yml
index dfadb371..db977360 100644
--- a/tests/modules/rseqc/junctionsaturation/test.yml
+++ b/tests/modules/rseqc/junctionsaturation/test.yml
@@ -1,5 +1,5 @@
- name: rseqc junctionsaturation test_rseqc_junctionsaturation
- command: nextflow run tests/modules/rseqc/junctionsaturation -entry test_rseqc_junctionsaturation -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/junctionsaturation -entry test_rseqc_junctionsaturation -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/junctionsaturation/nextflow.config
tags:
- rseqc/junctionsaturation
- rseqc
diff --git a/tests/modules/rseqc/readdistribution/main.nf b/tests/modules/rseqc/readdistribution/main.nf
index 415aed9a..180367f2 100644
--- a/tests/modules/rseqc/readdistribution/main.nf
+++ b/tests/modules/rseqc/readdistribution/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_READDISTRIBUTION } from '../../../../modules/rseqc/readdistribution/main.nf' addParams(options: [:])
+include { RSEQC_READDISTRIBUTION } from '../../../../modules/rseqc/readdistribution/main.nf'
workflow test_rseqc_readdistribution {
input = [ [ id:'test', single_end: false ], // meta map
diff --git a/tests/modules/rseqc/readdistribution/nextflow.config b/tests/modules/rseqc/readdistribution/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/readdistribution/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/readdistribution/test.yml b/tests/modules/rseqc/readdistribution/test.yml
index 79e7e1d3..e530e92a 100644
--- a/tests/modules/rseqc/readdistribution/test.yml
+++ b/tests/modules/rseqc/readdistribution/test.yml
@@ -1,5 +1,5 @@
- name: rseqc readdistribution test_rseqc_readdistribution
- command: nextflow run tests/modules/rseqc/readdistribution -entry test_rseqc_readdistribution -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/readdistribution -entry test_rseqc_readdistribution -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/readdistribution/nextflow.config
tags:
- rseqc
- rseqc/readdistribution
diff --git a/tests/modules/rseqc/readduplication/main.nf b/tests/modules/rseqc/readduplication/main.nf
index b94f6945..bcccde5d 100644
--- a/tests/modules/rseqc/readduplication/main.nf
+++ b/tests/modules/rseqc/readduplication/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { RSEQC_READDUPLICATION } from '../../../../modules/rseqc/readduplication/main.nf' addParams(options: [:])
+include { RSEQC_READDUPLICATION } from '../../../../modules/rseqc/readduplication/main.nf'
workflow test_rseqc_readduplication {
input = [ [ id:'test', single_end: false ], // meta map
diff --git a/tests/modules/rseqc/readduplication/nextflow.config b/tests/modules/rseqc/readduplication/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/rseqc/readduplication/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/rseqc/readduplication/test.yml b/tests/modules/rseqc/readduplication/test.yml
index 2a4c9546..b0c35071 100644
--- a/tests/modules/rseqc/readduplication/test.yml
+++ b/tests/modules/rseqc/readduplication/test.yml
@@ -1,5 +1,5 @@
- name: rseqc readduplication test_rseqc_readduplication
- command: nextflow run tests/modules/rseqc/readduplication -entry test_rseqc_readduplication -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/rseqc/readduplication -entry test_rseqc_readduplication -c ./tests/config/nextflow.config -c ./tests/modules/rseqc/readduplication/nextflow.config
tags:
- rseqc/readduplication
- rseqc
diff --git a/tests/modules/salmon/index/main.nf b/tests/modules/salmon/index/main.nf
index 98804733..680b4c6e 100644
--- a/tests/modules/salmon/index/main.nf
+++ b/tests/modules/salmon/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' addParams( options: [publish_dir:'salmon'] )
+include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf'
workflow test_salmon_index {
genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/salmon/index/nextflow.config b/tests/modules/salmon/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/salmon/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/salmon/index/test.yml b/tests/modules/salmon/index/test.yml
index acefb044..07815e37 100644
--- a/tests/modules/salmon/index/test.yml
+++ b/tests/modules/salmon/index/test.yml
@@ -1,5 +1,5 @@
- name: salmon index
- command: nextflow run ./tests/modules/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/salmon/index -entry test_salmon_index -c ./tests/config/nextflow.config -c ./tests/modules/salmon/index/nextflow.config
tags:
- salmon
- salmon/index
diff --git a/tests/modules/salmon/quant/main.nf b/tests/modules/salmon/quant/main.nf
index ad15870c..a970f6c5 100644
--- a/tests/modules/salmon/quant/main.nf
+++ b/tests/modules/salmon/quant/main.nf
@@ -2,14 +2,17 @@
nextflow.enable.dsl = 2
-include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf' addParams( options: [:] )
-include { SALMON_QUANT } from '../../../../modules/salmon/quant/main.nf' addParams( options: [args: '--minAssignedFrags 1'] )
+include { SALMON_INDEX } from '../../../../modules/salmon/index/main.nf'
+include { SALMON_QUANT } from '../../../../modules/salmon/quant/main.nf'
workflow test_salmon_quant_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
@@ -21,10 +24,13 @@ workflow test_salmon_quant_single_end {
workflow test_salmon_quant_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
@@ -36,9 +42,12 @@ workflow test_salmon_quant_paired_end {
workflow test_salmon_quant_single_end_lib_type_A {
- input = [ [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
genome_fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
transcript_fasta = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
diff --git a/tests/modules/salmon/quant/nextflow.config b/tests/modules/salmon/quant/nextflow.config
new file mode 100644
index 00000000..7a8c911a
--- /dev/null
+++ b/tests/modules/salmon/quant/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SALMON_QUANT {
+ ext.args = '--minAssignedFrags 1'
+ }
+
+}
diff --git a/tests/modules/salmon/quant/test.yml b/tests/modules/salmon/quant/test.yml
index d7ed0d0f..514718fa 100644
--- a/tests/modules/salmon/quant/test.yml
+++ b/tests/modules/salmon/quant/test.yml
@@ -1,5 +1,5 @@
- name: salmon quant single-end
- command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_single_end -c ./tests/config/nextflow.config -c ./tests/modules/salmon/quant/nextflow.config
tags:
- salmon
- salmon/quant
@@ -23,34 +23,34 @@
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/test/libParams/flenDist.txt
md5sum: 2de170bdc9f6fd237d286429b292bb28
- - path: ./output/index/salmon/ref_indexing.log
- - path: ./output/index/salmon/refseq.bin
+ - path: ./output/salmon/salmon/ref_indexing.log
+ - path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- - path: ./output/index/salmon/versionInfo.json
+ - path: ./output/salmon/salmon/versionInfo.json
md5sum: 6c764bd219b7bc17168a99d232c0fe09
- - path: ./output/index/salmon/complete_ref_lens.bin
+ - path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- - path: ./output/index/salmon/mphf.bin
+ - path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- - path: ./output/index/salmon/pre_indexing.log
- - path: ./output/index/salmon/ctable.bin
- - path: ./output/index/salmon/duplicate_clusters.tsv
+ - path: ./output/salmon/salmon/pre_indexing.log
+ - path: ./output/salmon/salmon/ctable.bin
+ - path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- - path: ./output/index/salmon/reflengths.bin
+ - path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- - path: ./output/index/salmon/info.json
+ - path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- - path: ./output/index/salmon/refAccumLengths.bin
+ - path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- - path: ./output/index/salmon/ctg_offsets.bin
+ - path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- - path: ./output/index/salmon/rank.bin
+ - path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- - path: ./output/index/salmon/pos.bin
- - path: ./output/index/salmon/seq.bin
+ - path: ./output/salmon/salmon/pos.bin
+ - path: ./output/salmon/salmon/seq.bin
- name: salmon quant paired end
- command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/salmon/quant/nextflow.config
tags:
- salmon
- salmon/quant
@@ -74,35 +74,35 @@
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: ./output/salmon/test/libParams/flenDist.txt
md5sum: 221f754ed55dd1e34874f9b7b3f9d240
- - path: ./output/index/salmon/ref_indexing.log
- - path: ./output/index/salmon/refseq.bin
+ - path: ./output/salmon/salmon/ref_indexing.log
+ - path: ./output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- - path: ./output/index/salmon/versionInfo.json
+ - path: ./output/salmon/salmon/versionInfo.json
md5sum: 6c764bd219b7bc17168a99d232c0fe09
- - path: ./output/index/salmon/complete_ref_lens.bin
+ - path: ./output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- - path: ./output/index/salmon/mphf.bin
+ - path: ./output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- - path: ./output/index/salmon/pre_indexing.log
- - path: ./output/index/salmon/ctable.bin
- - path: ./output/index/salmon/duplicate_clusters.tsv
+ - path: ./output/salmon/salmon/pre_indexing.log
+ - path: ./output/salmon/salmon/ctable.bin
+ - path: ./output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- - path: ./output/index/salmon/reflengths.bin
+ - path: ./output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- - path: ./output/index/salmon/info.json
+ - path: ./output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- - path: ./output/index/salmon/refAccumLengths.bin
+ - path: ./output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- - path: ./output/index/salmon/ctg_offsets.bin
+ - path: ./output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- - path: ./output/index/salmon/rank.bin
+ - path: ./output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- - path: ./output/index/salmon/pos.bin
- - path: ./output/index/salmon/seq.bin
+ - path: ./output/salmon/salmon/pos.bin
+ - path: ./output/salmon/salmon/seq.bin
- name: salmon quant test_salmon_quant_single_end_lib_type_A
- command: nextflow run tests/modules/salmon/quant -entry test_salmon_quant_single_end_lib_type_A -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/salmon/quant -entry test_salmon_quant_single_end_lib_type_A -c ./tests/config/nextflow.config -c ./tests/modules/salmon/quant/nextflow.config
tags:
- salmon/quant
- salmon
@@ -126,26 +126,26 @@
md5sum: ef13c06a538e9c34ca9f84212c82f44e
- path: output/salmon/test/libParams/flenDist.txt
md5sum: 2de170bdc9f6fd237d286429b292bb28
- - path: ./output/index/salmon/ref_indexing.log
- - path: output/index/salmon/refseq.bin
+ - path: ./output/salmon/salmon/ref_indexing.log
+ - path: output/salmon/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- - path: output/index/salmon/versionInfo.json
+ - path: output/salmon/salmon/versionInfo.json
md5sum: 6c764bd219b7bc17168a99d232c0fe09
- - path: output/index/salmon/complete_ref_lens.bin
+ - path: output/salmon/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- - path: output/index/salmon/mphf.bin
+ - path: output/salmon/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714
- - path: output/index/salmon/duplicate_clusters.tsv
+ - path: output/salmon/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c
- - path: output/index/salmon/reflengths.bin
+ - path: output/salmon/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08
- - path: output/index/salmon/info.json
+ - path: output/salmon/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f
- - path: output/index/salmon/refAccumLengths.bin
+ - path: output/salmon/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- - path: output/index/salmon/ctg_offsets.bin
+ - path: output/salmon/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25
- - path: output/index/salmon/rank.bin
+ - path: output/salmon/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- - path: ./output/index/salmon/pos.bin
- - path: ./output/index/salmon/seq.bin
+ - path: ./output/salmon/salmon/pos.bin
+ - path: ./output/salmon/salmon/seq.bin
diff --git a/tests/modules/samblaster/main.nf b/tests/modules/samblaster/main.nf
index 5983d130..5831ecfc 100644
--- a/tests/modules/samblaster/main.nf
+++ b/tests/modules/samblaster/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMBLASTER } from '../../../modules/samblaster/main.nf' addParams( options: [args: "-M --addMateTags", suffix:'.processed'] )
+include { SAMBLASTER } from '../../../modules/samblaster/main.nf'
workflow test_samblaster {
diff --git a/tests/modules/samblaster/nextflow.config b/tests/modules/samblaster/nextflow.config
new file mode 100644
index 00000000..3018088b
--- /dev/null
+++ b/tests/modules/samblaster/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMBLASTER {
+ ext.args = '-M --addMateTags'
+ ext.suffix = '.processed'
+ }
+
+}
diff --git a/tests/modules/samblaster/test.yml b/tests/modules/samblaster/test.yml
index d56d4330..acc6d0f0 100644
--- a/tests/modules/samblaster/test.yml
+++ b/tests/modules/samblaster/test.yml
@@ -1,5 +1,5 @@
- name: samblaster test_samblaster
- command: nextflow run tests/modules/samblaster -entry test_samblaster -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samblaster -entry test_samblaster -c ./tests/config/nextflow.config -c ./tests/modules/samblaster/nextflow.config
tags:
- samblaster
files:
diff --git a/tests/modules/samtools/ampliconclip/main.nf b/tests/modules/samtools/ampliconclip/main.nf
index a8d8609f..eae70b06 100644
--- a/tests/modules/samtools/ampliconclip/main.nf
+++ b/tests/modules/samtools/ampliconclip/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf' addParams([:])
+include { SAMTOOLS_AMPLICONCLIP } from '../../../../modules/samtools/ampliconclip/main.nf'
workflow test_samtools_ampliconclip_no_stats_no_rejects {
diff --git a/tests/modules/samtools/ampliconclip/nextflow.config b/tests/modules/samtools/ampliconclip/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/ampliconclip/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/ampliconclip/test.yml b/tests/modules/samtools/ampliconclip/test.yml
index 9e8e1f9f..e8fd456c 100644
--- a/tests/modules/samtools/ampliconclip/test.yml
+++ b/tests/modules/samtools/ampliconclip/test.yml
@@ -1,7 +1,5 @@
-## TODO nf-core: Please run the following command to build this file:
-# nf-core modules create-test-yml samtools/ampliconclip
- name: samtools ampliconclip no stats no rejects
- command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_no_rejects -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_no_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
tags:
- samtools
- samtools/ampliconclip
@@ -10,7 +8,7 @@
md5sum: 678f9ab04fbe3206f0f96e170fd833e9
- name: samtools ampliconclip no stats with rejects
- command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
tags:
- samtools
- samtools/ampliconclip
@@ -21,7 +19,7 @@
md5sum: a0bee15aead020d16d0c81bd9667df46
- name: samtools ampliconclip with stats with rejects
- command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
tags:
- samtools
- samtools/ampliconclip
diff --git a/tests/modules/samtools/bam2fq/main.nf b/tests/modules/samtools/bam2fq/main.nf
index f8614ad0..928bfe08 100644
--- a/tests/modules/samtools/bam2fq/main.nf
+++ b/tests/modules/samtools/bam2fq/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_BAM2FQ } from '../../../../modules/samtools/bam2fq/main.nf' addParams( options: [args: "-T RX"] )
+include { SAMTOOLS_BAM2FQ } from '../../../../modules/samtools/bam2fq/main.nf'
workflow test_samtools_bam2fq_nosplit {
diff --git a/tests/modules/samtools/bam2fq/nextflow.config b/tests/modules/samtools/bam2fq/nextflow.config
new file mode 100644
index 00000000..cf886bb2
--- /dev/null
+++ b/tests/modules/samtools/bam2fq/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_BAM2FQ {
+ ext.args = '-T RX'
+ }
+
+}
diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml
index ff1762b3..feb994fd 100644
--- a/tests/modules/samtools/bam2fq/test.yml
+++ b/tests/modules/samtools/bam2fq/test.yml
@@ -1,5 +1,5 @@
- name: samtools bam2fq test_samtools_bam2fq_nosplit
- command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config
tags:
- samtools/bam2fq
- samtools
@@ -8,7 +8,7 @@
md5sum: d733e66d29a4b366bf9df8c42f845256
- name: samtools bam2fq test_samtools_bam2fq_withsplit
- command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config
tags:
- samtools/bam2fq
- samtools
diff --git a/tests/modules/samtools/depth/main.nf b/tests/modules/samtools/depth/main.nf
index 90497534..c6d2dc0e 100644
--- a/tests/modules/samtools/depth/main.nf
+++ b/tests/modules/samtools/depth/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_DEPTH } from '../../../../modules/samtools/depth/main.nf' addParams( options: [:] )
+include { SAMTOOLS_DEPTH } from '../../../../modules/samtools/depth/main.nf'
workflow test_samtools_depth {
diff --git a/tests/modules/samtools/depth/nextflow.config b/tests/modules/samtools/depth/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/depth/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/depth/test.yml b/tests/modules/samtools/depth/test.yml
index 4d5007c8..978134ad 100644
--- a/tests/modules/samtools/depth/test.yml
+++ b/tests/modules/samtools/depth/test.yml
@@ -1,5 +1,5 @@
- name: samtools depth
- command: nextflow run tests/modules/samtools/depth -entry test_samtools_depth -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/depth -entry test_samtools_depth -c ./tests/config/nextflow.config -c ./tests/modules/samtools/depth/nextflow.config
tags:
- samtools/depth
- samtools
diff --git a/tests/modules/samtools/faidx/main.nf b/tests/modules/samtools/faidx/main.nf
index 0102af28..bc47c847 100644
--- a/tests/modules/samtools/faidx/main.nf
+++ b/tests/modules/samtools/faidx/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_FAIDX } from '../../../../modules/samtools/faidx/main.nf' addParams( options: [:] )
+include { SAMTOOLS_FAIDX } from '../../../../modules/samtools/faidx/main.nf'
workflow test_samtools_faidx {
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/samtools/faidx/nextflow.config b/tests/modules/samtools/faidx/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/faidx/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/faidx/test.yml b/tests/modules/samtools/faidx/test.yml
index 49a92265..f0224f34 100644
--- a/tests/modules/samtools/faidx/test.yml
+++ b/tests/modules/samtools/faidx/test.yml
@@ -1,5 +1,5 @@
- name: samtools faidx test workflow
- command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/faidx -entry test_samtools_faidx -c ./tests/config/nextflow.config -c ./tests/modules/samtools/faidx/nextflow.config
tags:
- samtools
- samtools/faidx
diff --git a/tests/modules/samtools/fastq/main.nf b/tests/modules/samtools/fastq/main.nf
index 94ad9471..6e7e323c 100644
--- a/tests/modules/samtools/fastq/main.nf
+++ b/tests/modules/samtools/fastq/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_FASTQ } from '../../../../modules/samtools/fastq/main.nf' addParams( options: [:] )
+include { SAMTOOLS_FASTQ } from '../../../../modules/samtools/fastq/main.nf'
workflow test_samtools_fastq {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/fastq/nextflow.config b/tests/modules/samtools/fastq/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/fastq/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/fastq/test.yml b/tests/modules/samtools/fastq/test.yml
index bfcf5c92..39da9889 100644
--- a/tests/modules/samtools/fastq/test.yml
+++ b/tests/modules/samtools/fastq/test.yml
@@ -1,5 +1,5 @@
- name: samtools fastq test_samtools_fastq
- command: nextflow run tests/modules/samtools/fastq -entry test_samtools_fastq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/fastq -entry test_samtools_fastq -c ./tests/config/nextflow.config -c ./tests/modules/samtools/fastq/nextflow.config
tags:
- samtools
- samtools/fastq
diff --git a/tests/modules/samtools/fixmate/main.nf b/tests/modules/samtools/fixmate/main.nf
index 5174beab..cb7c136d 100644
--- a/tests/modules/samtools/fixmate/main.nf
+++ b/tests/modules/samtools/fixmate/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf' addParams( options: [args:'-r -c -m'] )
+include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf'
workflow test_samtools_fixmate {
diff --git a/tests/modules/samtools/fixmate/nextflow.config b/tests/modules/samtools/fixmate/nextflow.config
new file mode 100644
index 00000000..b9402bcf
--- /dev/null
+++ b/tests/modules/samtools/fixmate/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_FIXMATE {
+ ext.args = '-r -c -m'
+ }
+
+}
diff --git a/tests/modules/samtools/fixmate/test.yml b/tests/modules/samtools/fixmate/test.yml
index 0b3aa2a9..8e87e059 100644
--- a/tests/modules/samtools/fixmate/test.yml
+++ b/tests/modules/samtools/fixmate/test.yml
@@ -1,5 +1,5 @@
- name: samtools fixmate test_samtools_fixmate
- command: nextflow run tests/modules/samtools/fixmate -entry test_samtools_fixmate -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/fixmate -entry test_samtools_fixmate -c ./tests/config/nextflow.config -c ./tests/modules/samtools/fixmate/nextflow.config
tags:
- samtools
- samtools/fixmate
diff --git a/tests/modules/samtools/flagstat/main.nf b/tests/modules/samtools/flagstat/main.nf
index a31a7d22..a0e86422 100644
--- a/tests/modules/samtools/flagstat/main.nf
+++ b/tests/modules/samtools/flagstat/main.nf
@@ -2,13 +2,14 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_FLAGSTAT } from '../../../../modules/samtools/flagstat/main.nf' addParams( options: [:] )
+include { SAMTOOLS_FLAGSTAT } from '../../../../modules/samtools/flagstat/main.nf'
workflow test_samtools_flagstat {
- input = [ [ id:'test', single_end:false ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+ ]
SAMTOOLS_FLAGSTAT ( input )
}
diff --git a/tests/modules/samtools/flagstat/nextflow.config b/tests/modules/samtools/flagstat/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/flagstat/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/flagstat/test.yml b/tests/modules/samtools/flagstat/test.yml
index 0da6c2f4..a5f28b36 100644
--- a/tests/modules/samtools/flagstat/test.yml
+++ b/tests/modules/samtools/flagstat/test.yml
@@ -1,5 +1,5 @@
- name: samtools flagstat
- command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/samtools/flagstat/nextflow.config
tags:
- samtools
- samtools/flagstat
diff --git a/tests/modules/samtools/idxstats/main.nf b/tests/modules/samtools/idxstats/main.nf
index 9919c3e4..f3de76a0 100644
--- a/tests/modules/samtools/idxstats/main.nf
+++ b/tests/modules/samtools/idxstats/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_IDXSTATS } from '../../../../modules/samtools/idxstats/main.nf' addParams( options: [:] )
+include { SAMTOOLS_IDXSTATS } from '../../../../modules/samtools/idxstats/main.nf'
workflow test_samtools_idxstats {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/idxstats/nextflow.config b/tests/modules/samtools/idxstats/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/idxstats/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/idxstats/test.yml b/tests/modules/samtools/idxstats/test.yml
index 6064ca56..88786eef 100644
--- a/tests/modules/samtools/idxstats/test.yml
+++ b/tests/modules/samtools/idxstats/test.yml
@@ -1,5 +1,5 @@
- name: samtools idxstats
- command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/idxstats -entry test_samtools_idxstats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/idxstats/nextflow.config
tags:
- samtools
- samtools/idxstats
diff --git a/tests/modules/samtools/index/main.nf b/tests/modules/samtools/index/main.nf
index 737936fb..3592a99a 100644
--- a/tests/modules/samtools/index/main.nf
+++ b/tests/modules/samtools/index/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/samtools/index/main.nf' addParams( options: [:] )
-include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/samtools/index/main.nf' addParams( options: [args:'-c'] )
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_BAI } from '../../../../modules/samtools/index/main.nf'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CRAI } from '../../../../modules/samtools/index/main.nf'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_CSI } from '../../../../modules/samtools/index/main.nf'
workflow test_samtools_index_bai {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/index/nextflow.config b/tests/modules/samtools/index/nextflow.config
new file mode 100644
index 00000000..d3a4c785
--- /dev/null
+++ b/tests/modules/samtools/index/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_INDEX_CSI {
+ ext.args = '-c'
+ }
+
+}
diff --git a/tests/modules/samtools/index/test.yml b/tests/modules/samtools/index/test.yml
index 279b99d8..6972ed65 100644
--- a/tests/modules/samtools/index/test.yml
+++ b/tests/modules/samtools/index/test.yml
@@ -1,5 +1,5 @@
- name: samtools index test_samtools_index_bai
- command: nextflow run tests/modules/samtools/index -entry test_samtools_index_bai -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_bai -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config
tags:
- samtools
- samtools/index
@@ -8,7 +8,7 @@
md5sum: 704c10dd1326482448ca3073fdebc2f4
- name: samtools index test_samtools_index_crai
- command: nextflow run tests/modules/samtools/index -entry test_samtools_index_crai -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_crai -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config
tags:
- samtools
- samtools/index
@@ -17,7 +17,7 @@
md5sum: 537e3d8c937bcc4e34e1cf47cd71d484
- name: samtools index test_samtools_index_csi
- command: nextflow run tests/modules/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config
tags:
- samtools
- samtools/index
diff --git a/tests/modules/samtools/merge/main.nf b/tests/modules/samtools/merge/main.nf
index 07485df1..ad5c56e3 100644
--- a/tests/modules/samtools/merge/main.nf
+++ b/tests/modules/samtools/merge/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf' addParams( options: [suffix:'_merged'] )
+include { SAMTOOLS_MERGE } from '../../../../modules/samtools/merge/main.nf'
workflow test_samtools_merge {
input = [ [ id: 'test' ], // meta map
diff --git a/tests/modules/samtools/merge/nextflow.config b/tests/modules/samtools/merge/nextflow.config
new file mode 100644
index 00000000..cb350bf7
--- /dev/null
+++ b/tests/modules/samtools/merge/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_MERGE {
+ ext.suffix = '_merged'
+ }
+
+}
diff --git a/tests/modules/samtools/merge/test.yml b/tests/modules/samtools/merge/test.yml
index f04aa74b..948c6191 100644
--- a/tests/modules/samtools/merge/test.yml
+++ b/tests/modules/samtools/merge/test.yml
@@ -1,5 +1,5 @@
- name: samtools merge test_samtools_merge
- command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
tags:
- samtools
- samtools/merge
@@ -7,7 +7,7 @@
- path: output/samtools/test_merged.bam
- name: samtools merge test_samtools_merge_cram
- command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/merge -entry test_samtools_merge_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/merge/nextflow.config
tags:
- samtools
- samtools/merge
diff --git a/tests/modules/samtools/mpileup/main.nf b/tests/modules/samtools/mpileup/main.nf
index b8db0275..dc58cc2c 100644
--- a/tests/modules/samtools/mpileup/main.nf
+++ b/tests/modules/samtools/mpileup/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf' addParams( options: [:] )
+include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf'
workflow test_samtools_mpileup {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/mpileup/nextflow.config b/tests/modules/samtools/mpileup/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/mpileup/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/mpileup/test.yml b/tests/modules/samtools/mpileup/test.yml
index 25c39d63..53a9c142 100644
--- a/tests/modules/samtools/mpileup/test.yml
+++ b/tests/modules/samtools/mpileup/test.yml
@@ -1,5 +1,5 @@
- name: samtools mpileup
- command: nextflow run ./tests/modules/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/mpileup -entry test_samtools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/samtools/mpileup/nextflow.config
tags:
- samtools
- samtools/mpileup
diff --git a/tests/modules/samtools/sort/main.nf b/tests/modules/samtools/sort/main.nf
index b76cdb1a..9853b355 100644
--- a/tests/modules/samtools/sort/main.nf
+++ b/tests/modules/samtools/sort/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_SORT } from '../../../../modules/samtools/sort/main.nf' addParams( options: ['suffix': '.sorted'] )
+include { SAMTOOLS_SORT } from '../../../../modules/samtools/sort/main.nf'
workflow test_samtools_sort {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/sort/nextflow.config b/tests/modules/samtools/sort/nextflow.config
new file mode 100644
index 00000000..57ae6280
--- /dev/null
+++ b/tests/modules/samtools/sort/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SAMTOOLS_SORT {
+ ext.suffix = '.sorted'
+ }
+
+}
diff --git a/tests/modules/samtools/sort/test.yml b/tests/modules/samtools/sort/test.yml
index 785ec03b..dfd2eb69 100644
--- a/tests/modules/samtools/sort/test.yml
+++ b/tests/modules/samtools/sort/test.yml
@@ -1,5 +1,5 @@
- name: samtools sort
- command: nextflow run tests/modules/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/sort -entry test_samtools_sort -c ./tests/config/nextflow.config -c ./tests/modules/samtools/sort/nextflow.config
tags:
- samtools
- samtools/sort
diff --git a/tests/modules/samtools/stats/main.nf b/tests/modules/samtools/stats/main.nf
index 4e92b366..d83cbf4a 100644
--- a/tests/modules/samtools/stats/main.nf
+++ b/tests/modules/samtools/stats/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_STATS } from '../../../../modules/samtools/stats/main.nf' addParams( options: [:] )
+include { SAMTOOLS_STATS } from '../../../../modules/samtools/stats/main.nf'
workflow test_samtools_stats {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/stats/nextflow.config b/tests/modules/samtools/stats/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/stats/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml
index c186665a..178eba72 100644
--- a/tests/modules/samtools/stats/test.yml
+++ b/tests/modules/samtools/stats/test.yml
@@ -1,5 +1,5 @@
- name: samtools stats test_samtools_stats
- command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
tags:
- samtools/stats
- samtools
@@ -8,7 +8,7 @@
md5sum: 09146eeecfcae2a84fb8615c86cd8d64
- name: samtools stats test_samtools_stats_cram
- command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
tags:
- samtools/stats
- samtools
diff --git a/tests/modules/samtools/view/main.nf b/tests/modules/samtools/view/main.nf
index bd270cd8..8ee27ef8 100644
--- a/tests/modules/samtools/view/main.nf
+++ b/tests/modules/samtools/view/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf' addParams( options: [:] )
+include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
workflow test_samtools_view {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/samtools/view/nextflow.config b/tests/modules/samtools/view/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/view/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/view/test.yml b/tests/modules/samtools/view/test.yml
index ceaa0e89..1287d455 100644
--- a/tests/modules/samtools/view/test.yml
+++ b/tests/modules/samtools/view/test.yml
@@ -1,5 +1,5 @@
- name: samtools view test_samtools_view
- command: nextflow run tests/modules/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config
tags:
- samtools/view
- samtools
@@ -8,7 +8,7 @@
md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
- name: samtools view test_samtools_view_cram
- command: nextflow run tests/modules/samtools/view -entry test_samtools_view_cram -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config
tags:
- samtools/view
- samtools
diff --git a/tests/modules/scoary/main.nf b/tests/modules/scoary/main.nf
index ec3f6e9f..5f080b7d 100644
--- a/tests/modules/scoary/main.nf
+++ b/tests/modules/scoary/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SCOARY } from '../../../modules/scoary/main.nf' addParams( options: [:] )
+include { SCOARY } from '../../../modules/scoary/main.nf'
workflow test_scoary {
diff --git a/tests/modules/scoary/nextflow.config b/tests/modules/scoary/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/scoary/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/scoary/test.yml b/tests/modules/scoary/test.yml
index c5269293..71344093 100644
--- a/tests/modules/scoary/test.yml
+++ b/tests/modules/scoary/test.yml
@@ -1,5 +1,5 @@
- name: scoary test_scoary
- command: nextflow run tests/modules/scoary -entry test_scoary -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/scoary -entry test_scoary -c ./tests/config/nextflow.config -c ./tests/modules/scoary/nextflow.config
tags:
- scoary
files:
diff --git a/tests/modules/seacr/callpeak/main.nf b/tests/modules/seacr/callpeak/main.nf
index a1aeb76e..230d3a4c 100644
--- a/tests/modules/seacr/callpeak/main.nf
+++ b/tests/modules/seacr/callpeak/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf' addParams( options: [ args:'norm stringent' ] )
+include { SEACR_CALLPEAK } from '../../../../modules/seacr/callpeak/main.nf'
workflow test_seacr_callpeak {
input = [ [ id:'test_1'],
diff --git a/tests/modules/seacr/callpeak/nextflow.config b/tests/modules/seacr/callpeak/nextflow.config
new file mode 100644
index 00000000..54c19e6b
--- /dev/null
+++ b/tests/modules/seacr/callpeak/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEACR_CALLPEAK {
+ ext.args = 'norm stringent'
+ }
+
+}
diff --git a/tests/modules/seacr/callpeak/test.yml b/tests/modules/seacr/callpeak/test.yml
index 2cf75b06..63104bd0 100644
--- a/tests/modules/seacr/callpeak/test.yml
+++ b/tests/modules/seacr/callpeak/test.yml
@@ -1,5 +1,5 @@
- name: seacr callpeak
- command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak -c ./tests/config/nextflow.config -c ./tests/modules/seacr/callpeak/nextflow.config
tags:
- seacr
- seacr/callpeak
@@ -8,7 +8,7 @@
md5sum: a3cb0c7c4ffa895788da3f0d6371b7df
- name: seacr callpeak threshold
- command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak_threshold -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seacr/callpeak -entry test_seacr_callpeak_threshold -c ./tests/config/nextflow.config -c ./tests/modules/seacr/callpeak/nextflow.config
tags:
- seacr
- seacr/callpeak
diff --git a/tests/modules/seqkit/split2/main.nf b/tests/modules/seqkit/split2/main.nf
index 21626cac..acb9d41b 100644
--- a/tests/modules/seqkit/split2/main.nf
+++ b/tests/modules/seqkit/split2/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../modules/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 8K'] )
-include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../modules/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 50' ] )
-include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../modules/seqkit/split2/main.nf' addParams( options: ['args': '--by-part 3'] )
+include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../modules/seqkit/split2/main.nf'
+include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../modules/seqkit/split2/main.nf'
+include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../modules/seqkit/split2/main.nf'
workflow test_seqkit_split2_single_end_length {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/seqkit/split2/nextflow.config b/tests/modules/seqkit/split2/nextflow.config
new file mode 100644
index 00000000..e4f64931
--- /dev/null
+++ b/tests/modules/seqkit/split2/nextflow.config
@@ -0,0 +1,17 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEQKIT_SPLIT2_LENGTH {
+ ext.args = '--by-length 8K'
+ }
+
+ withName: SEQKIT_SPLIT2_SIZE {
+ ext.args = '--by-size 50'
+ }
+
+ withName: SEQKIT_SPLIT2_PART {
+ ext.args = '--by-part 3'
+ }
+
+}
diff --git a/tests/modules/seqkit/split2/test.yml b/tests/modules/seqkit/split2/test.yml
index 13f3b003..12b02072 100644
--- a/tests/modules/seqkit/split2/test.yml
+++ b/tests/modules/seqkit/split2/test.yml
@@ -1,5 +1,5 @@
- name: seqkit split2 single-end length
- command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_length -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
tags:
- seqkit
- seqkit/split2
@@ -10,7 +10,7 @@
md5sum: cf38c51506e45380fe25abdd1bd5ccc6
- name: seqkit split2 single-end size
- command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_size -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
tags:
- seqkit
- seqkit/split2
@@ -21,7 +21,7 @@
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
- name: seqkit split2 single-end part
- command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_single_end_part -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
tags:
- seqkit
- seqkit/split2
@@ -34,7 +34,7 @@
md5sum: 8bc86ba83a611c54f592f4eae19b680f
- name: seqkit split2 paired-end length
- command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
tags:
- seqkit
- seqkit/split2
@@ -49,7 +49,7 @@
md5sum: 927097c6ac7522199a9e016333181a8e
- name: seqkit split2 paired-end size
- command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
tags:
- seqkit
- seqkit/split2
@@ -64,7 +64,7 @@
md5sum: 8796c3f327b1094244bfcdb36d536526
- name: seqkit split2 paired-end part
- command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c ./tests/config/nextflow.config -c ./tests/modules/seqkit/split2/nextflow.config
tags:
- seqkit
- seqkit/split2
diff --git a/tests/modules/seqsero2/main.nf b/tests/modules/seqsero2/main.nf
index 04ee8e27..9587bf9f 100644
--- a/tests/modules/seqsero2/main.nf
+++ b/tests/modules/seqsero2/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQSERO2 } from '../../../modules/seqsero2/main.nf' addParams( options: [args: '-m k -t 4'] )
+include { SEQSERO2 } from '../../../modules/seqsero2/main.nf'
workflow test_seqsero2 {
diff --git a/tests/modules/seqsero2/nextflow.config b/tests/modules/seqsero2/nextflow.config
new file mode 100644
index 00000000..b46fa7e2
--- /dev/null
+++ b/tests/modules/seqsero2/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEQSERO2 {
+ ext.args = '-m k -t 4'
+ }
+
+}
diff --git a/tests/modules/seqsero2/test.yml b/tests/modules/seqsero2/test.yml
index 2aa49686..e2dec062 100644
--- a/tests/modules/seqsero2/test.yml
+++ b/tests/modules/seqsero2/test.yml
@@ -1,5 +1,5 @@
- name: seqsero2 test_seqsero2
- command: nextflow run tests/modules/seqsero2 -entry test_seqsero2 -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqsero2 -entry test_seqsero2 -c ./tests/config/nextflow.config -c ./tests/modules/seqsero2/nextflow.config
tags:
- seqsero2
files:
diff --git a/tests/modules/seqtk/mergepe/main.nf b/tests/modules/seqtk/mergepe/main.nf
index 13654dc6..b8e12213 100644
--- a/tests/modules/seqtk/mergepe/main.nf
+++ b/tests/modules/seqtk/mergepe/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf' addParams( options: [ 'suffix':'.processed' ] )
+include { SEQTK_MERGEPE } from '../../../../modules/seqtk/mergepe/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/seqtk/mergepe/nextflow.config b/tests/modules/seqtk/mergepe/nextflow.config
new file mode 100644
index 00000000..b14e72ff
--- /dev/null
+++ b/tests/modules/seqtk/mergepe/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEQTK_MERGEPE {
+ ext.suffix = '.processed'
+ }
+
+}
diff --git a/tests/modules/seqtk/mergepe/test.yml b/tests/modules/seqtk/mergepe/test.yml
index 8ae95354..2a6d4d33 100644
--- a/tests/modules/seqtk/mergepe/test.yml
+++ b/tests/modules/seqtk/mergepe/test.yml
@@ -1,5 +1,5 @@
- name: seqtk mergepe test_seqtk_mergepe_single_end
- command: nextflow run tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_single_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/mergepe/nextflow.config
tags:
- seqtk/mergepe
- seqtk
@@ -8,7 +8,7 @@
md5sum: e325ef7deb4023447a1f074e285761af
- name: seqtk mergepe test_seqtk_mergepe_paired_end
- command: nextflow run tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/mergepe/nextflow.config
tags:
- seqtk/mergepe
- seqtk
diff --git a/tests/modules/seqtk/sample/main.nf b/tests/modules/seqtk/sample/main.nf
index 4508db84..6899ef62 100644
--- a/tests/modules/seqtk/sample/main.nf
+++ b/tests/modules/seqtk/sample/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQTK_SAMPLE } from '../../../../modules/seqtk/sample/main.nf' addParams( options: [ 'args': '-s100', 'suffix':'.sampled' ] )
+include { SEQTK_SAMPLE } from '../../../../modules/seqtk/sample/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/seqtk/sample/nextflow.config b/tests/modules/seqtk/sample/nextflow.config
new file mode 100644
index 00000000..3efac50d
--- /dev/null
+++ b/tests/modules/seqtk/sample/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEQTK_SAMPLE {
+ ext.args = '-s100'
+ ext.suffix = '.sampled'
+ }
+
+}
diff --git a/tests/modules/seqtk/sample/test.yml b/tests/modules/seqtk/sample/test.yml
index d4cf2ca9..df24b3a4 100644
--- a/tests/modules/seqtk/sample/test.yml
+++ b/tests/modules/seqtk/sample/test.yml
@@ -1,5 +1,5 @@
- name: seqtk sample test_seqtk_sample_single_end
- command: nextflow run tests/modules/seqtk/sample -entry test_seqtk_sample_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_single_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config
tags:
- seqtk
- seqtk/sample
@@ -8,7 +8,7 @@
md5sum: 73c3e8f113860244f3ed3866a8b9d555
- name: seqtk sample test_seqtk_sample_paired_end
- command: nextflow run tests/modules/seqtk/sample -entry test_seqtk_sample_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config
tags:
- seqtk
- seqtk/sample
diff --git a/tests/modules/seqtk/subseq/main.nf b/tests/modules/seqtk/subseq/main.nf
index 7c5dc7b2..608b7c2f 100644
--- a/tests/modules/seqtk/subseq/main.nf
+++ b/tests/modules/seqtk/subseq/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQTK_SUBSEQ } from '../../../../modules/seqtk/subseq/main.nf' addParams( options: ['suffix':'.filtered'] )
+include { SEQTK_SUBSEQ } from '../../../../modules/seqtk/subseq/main.nf'
workflow test_seqtk_subseq {
diff --git a/tests/modules/seqtk/subseq/nextflow.config b/tests/modules/seqtk/subseq/nextflow.config
new file mode 100644
index 00000000..c61c4a74
--- /dev/null
+++ b/tests/modules/seqtk/subseq/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEQTK_SUBSEQ {
+ ext.suffix = '.filtered'
+ }
+
+}
diff --git a/tests/modules/seqtk/subseq/test.yml b/tests/modules/seqtk/subseq/test.yml
index fca64804..4003e3ab 100644
--- a/tests/modules/seqtk/subseq/test.yml
+++ b/tests/modules/seqtk/subseq/test.yml
@@ -1,5 +1,5 @@
- name: seqtk subseq test_seqtk_subseq
- command: nextflow run tests/modules/seqtk/subseq -entry test_seqtk_subseq -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqtk/subseq -entry test_seqtk_subseq -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/subseq/nextflow.config
tags:
- seqtk
- seqtk/subseq
diff --git a/tests/modules/sequenzautils/bam2seqz/main.nf b/tests/modules/sequenzautils/bam2seqz/main.nf
index ae478b88..fcd4c7c7 100755
--- a/tests/modules/sequenzautils/bam2seqz/main.nf
+++ b/tests/modules/sequenzautils/bam2seqz/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/sequenzautils/bam2seqz/main.nf' addParams( options: [:] )
+include { SEQUENZAUTILS_BAM2SEQZ } from '../../../../modules/sequenzautils/bam2seqz/main.nf'
workflow test_sequenzautils_bam2seqz {
diff --git a/tests/modules/sequenzautils/bam2seqz/nextflow.config b/tests/modules/sequenzautils/bam2seqz/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/sequenzautils/bam2seqz/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/sequenzautils/bam2seqz/test.yml b/tests/modules/sequenzautils/bam2seqz/test.yml
index 0b9cac53..f3ea6cf0 100644
--- a/tests/modules/sequenzautils/bam2seqz/test.yml
+++ b/tests/modules/sequenzautils/bam2seqz/test.yml
@@ -1,5 +1,5 @@
- name: sequenzautils bam2seqz
- command: nextflow run ./tests/modules/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/sequenzautils/bam2seqz -entry test_sequenzautils_bam2seqz -c ./tests/config/nextflow.config -c ./tests/modules/sequenzautils/bam2seqz/nextflow.config
tags:
- sequenzautils
- sequenzautils/bam2seqz
diff --git a/tests/modules/sequenzautils/gcwiggle/main.nf b/tests/modules/sequenzautils/gcwiggle/main.nf
index e314f1e0..b25e037e 100644
--- a/tests/modules/sequenzautils/gcwiggle/main.nf
+++ b/tests/modules/sequenzautils/gcwiggle/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQUENZAUTILS_GCWIGGLE } from '../../../../modules/sequenzautils/gcwiggle/main.nf' addParams( options: [ 'args': '-w 50' ] )
+include { SEQUENZAUTILS_GCWIGGLE } from '../../../../modules/sequenzautils/gcwiggle/main.nf'
workflow test_sequenzautils_gcwiggle {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/sequenzautils/gcwiggle/nextflow.config b/tests/modules/sequenzautils/gcwiggle/nextflow.config
new file mode 100644
index 00000000..62e68935
--- /dev/null
+++ b/tests/modules/sequenzautils/gcwiggle/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SEQUENZAUTILS_GCWIGGLE {
+ ext.args = '-w 50'
+ }
+
+}
diff --git a/tests/modules/sequenzautils/gcwiggle/test.yml b/tests/modules/sequenzautils/gcwiggle/test.yml
index aa7a3167..21ddc4ab 100644
--- a/tests/modules/sequenzautils/gcwiggle/test.yml
+++ b/tests/modules/sequenzautils/gcwiggle/test.yml
@@ -1,7 +1,5 @@
-## TODO nf-core: Please run the following command to build this file:
-# nf-core modules create-test-yml sequenzautils/gcwiggle
- name: sequenzautils gcwiggle
- command: nextflow run ./tests/modules/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/sequenzautils/gcwiggle -entry test_sequenzautils_gcwiggle -c ./tests/config/nextflow.config -c ./tests/modules/sequenzautils/gcwiggle/nextflow.config
tags:
- sequenzautils
- sequenzautils/gcwiggle
diff --git a/tests/modules/seqwish/induce/main.nf b/tests/modules/seqwish/induce/main.nf
index 356ca705..6388fea2 100644
--- a/tests/modules/seqwish/induce/main.nf
+++ b/tests/modules/seqwish/induce/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SEQWISH_INDUCE } from '../../../../modules/seqwish/induce/main.nf' addParams( options: [:] )
+include { SEQWISH_INDUCE } from '../../../../modules/seqwish/induce/main.nf'
workflow test_seqwish_induce {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/seqwish/induce/nextflow.config b/tests/modules/seqwish/induce/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/seqwish/induce/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/seqwish/induce/test.yml b/tests/modules/seqwish/induce/test.yml
index d27de3c4..d5a8a7cd 100644
--- a/tests/modules/seqwish/induce/test.yml
+++ b/tests/modules/seqwish/induce/test.yml
@@ -1,5 +1,5 @@
- name: seqwish induce
- command: nextflow run ./tests/modules/seqwish/induce -entry test_seqwish_induce -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/seqwish/induce -entry test_seqwish_induce -c ./tests/config/nextflow.config -c ./tests/modules/seqwish/induce/nextflow.config
tags:
- seqwish
- seqwish/induce
diff --git a/tests/modules/shovill/main.nf b/tests/modules/shovill/main.nf
index acc65169..2416022f 100644
--- a/tests/modules/shovill/main.nf
+++ b/tests/modules/shovill/main.nf
@@ -2,10 +2,10 @@
nextflow.enable.dsl = 2
-include { SHOVILL } from '../../../modules/shovill/main.nf' addParams( options: [args: '--gsize 2800000 --kmers 31'] )
-include { SHOVILL as SHOVILL_SKESA } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler skesa --gsize 2800000'] )
-include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler megahit --gsize 2800000'] )
-include { SHOVILL as SHOVILL_VELVET } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler velvet --gsize 2800000'] )
+include { SHOVILL } from '../../../modules/shovill/main.nf'
+include { SHOVILL as SHOVILL_SKESA } from '../../../modules/shovill/main.nf'
+include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/shovill/main.nf'
+include { SHOVILL as SHOVILL_VELVET } from '../../../modules/shovill/main.nf'
workflow test_shovill {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/shovill/nextflow.config b/tests/modules/shovill/nextflow.config
new file mode 100644
index 00000000..0599f80b
--- /dev/null
+++ b/tests/modules/shovill/nextflow.config
@@ -0,0 +1,21 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SHOVILL {
+ ext.args = '--gsize 2800000 --kmers 31'
+ }
+
+ withName: SHOVILL_SKESA {
+ ext.args = '--assembler skesa --gsize 2800000'
+ }
+
+ withName: SHOVILL_MEGAHIT {
+ ext.args = '--assembler megahit --gsize 2800000'
+ }
+
+ withName: SHOVILL_VELVET {
+ ext.args = '--assembler velvet --gsize 2800000'
+ }
+
+}
diff --git a/tests/modules/shovill/test.yml b/tests/modules/shovill/test.yml
index a716bc66..6fdd2f3f 100644
--- a/tests/modules/shovill/test.yml
+++ b/tests/modules/shovill/test.yml
@@ -1,5 +1,5 @@
- name: shovill with spades
- command: nextflow run ./tests/modules/shovill -entry test_shovill -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/shovill -entry test_shovill -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
tags:
- shovill
files:
@@ -13,7 +13,7 @@
- path: output/shovill/shovill.log
- name: shovill with megahit
- command: nextflow run ./tests/modules/shovill -entry test_shovill_megahit -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/shovill -entry test_shovill_megahit -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
tags:
- shovill
files:
@@ -26,7 +26,7 @@
- path: output/shovill/shovill.log
- name: shovill with skesa
- command: nextflow run ./tests/modules/shovill -entry test_shovill_skesa -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/shovill -entry test_shovill_skesa -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
tags:
- shovill
files:
@@ -39,7 +39,7 @@
- path: output/shovill/shovill.log
- name: shovill with velvet
- command: nextflow run ./tests/modules/shovill -entry test_shovill_velvet -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/shovill -entry test_shovill_velvet -c ./tests/config/nextflow.config -c ./tests/modules/shovill/nextflow.config
tags:
- shovill
files:
diff --git a/tests/modules/snpdists/main.nf b/tests/modules/snpdists/main.nf
index 8a29effa..be6d745c 100644
--- a/tests/modules/snpdists/main.nf
+++ b/tests/modules/snpdists/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SNPDISTS } from '../../../modules/snpdists/main.nf' addParams( options: [:] )
+include { SNPDISTS } from '../../../modules/snpdists/main.nf'
workflow test_snpdists {
diff --git a/tests/modules/snpdists/nextflow.config b/tests/modules/snpdists/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/snpdists/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/snpdists/test.yml b/tests/modules/snpdists/test.yml
index d140ce6e..c23945ce 100644
--- a/tests/modules/snpdists/test.yml
+++ b/tests/modules/snpdists/test.yml
@@ -1,5 +1,5 @@
- name: snpdists
- command: nextflow run ./tests/modules/snpdists -entry test_snpdists -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/snpdists -entry test_snpdists -c ./tests/config/nextflow.config -c ./tests/modules/snpdists/nextflow.config
tags:
- snpdists
files:
diff --git a/tests/modules/snpeff/main.nf b/tests/modules/snpeff/main.nf
index 923f98f4..4e8a982d 100644
--- a/tests/modules/snpeff/main.nf
+++ b/tests/modules/snpeff/main.nf
@@ -2,11 +2,13 @@
nextflow.enable.dsl = 2
-include { SNPEFF } from '../../../modules/snpeff/main.nf' addParams( snpeff_tag: '5.0.WBcel235', use_cache: false )
+include { SNPEFF } from '../../../modules/snpeff/main.nf'
workflow test_snpeff {
- input = [ [ id:'test' ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test' ], // meta map
+ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+ ]
+
SNPEFF ( input, "WBcel235.99", [] )
}
diff --git a/tests/modules/snpeff/nextflow.config b/tests/modules/snpeff/nextflow.config
new file mode 100644
index 00000000..589c8cfb
--- /dev/null
+++ b/tests/modules/snpeff/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SNPEFF {
+ ext.snpeff_tag = '5.0.WBcel235'
+ ext.use_cache = false
+ }
+
+}
diff --git a/tests/modules/snpeff/test.yml b/tests/modules/snpeff/test.yml
index 44eba200..8f4d980f 100644
--- a/tests/modules/snpeff/test.yml
+++ b/tests/modules/snpeff/test.yml
@@ -1,5 +1,5 @@
- name: snpeff test_snpeff
- command: nextflow run tests/modules/snpeff -entry test_snpeff -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/snpeff -entry test_snpeff -c ./tests/config/nextflow.config -c ./tests/modules/snpeff/nextflow.config
tags:
- snpeff
files:
diff --git a/tests/modules/snpsites/main.nf b/tests/modules/snpsites/main.nf
index df2a6852..f7801673 100644
--- a/tests/modules/snpsites/main.nf
+++ b/tests/modules/snpsites/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SNPSITES } from '../../../modules/snpsites/main.nf' addParams( options: [:] )
+include { SNPSITES } from '../../../modules/snpsites/main.nf'
workflow test_snpsites {
diff --git a/tests/modules/snpsites/nextflow.config b/tests/modules/snpsites/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/snpsites/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/snpsites/test.yml b/tests/modules/snpsites/test.yml
index 8361cd05..d9c19cd5 100644
--- a/tests/modules/snpsites/test.yml
+++ b/tests/modules/snpsites/test.yml
@@ -1,5 +1,5 @@
- name: snpsites
- command: nextflow run ./tests/modules/snpsites -entry test_snpsites -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/snpsites -entry test_snpsites -c ./tests/config/nextflow.config -c ./tests/modules/snpsites/nextflow.config
tags:
- snpsites
files:
diff --git a/tests/modules/spades/main.nf b/tests/modules/spades/main.nf
index b09a4266..3710eeb7 100644
--- a/tests/modules/spades/main.nf
+++ b/tests/modules/spades/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SPADES } from '../../../modules/spades/main.nf' addParams( options: ['args': '--rnaviral'] )
+include { SPADES } from '../../../modules/spades/main.nf'
workflow test_spades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/spades/nextflow.config b/tests/modules/spades/nextflow.config
new file mode 100644
index 00000000..5fabafae
--- /dev/null
+++ b/tests/modules/spades/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SPADES {
+ ext.args = '--rnaviral'
+ }
+
+}
diff --git a/tests/modules/spades/test.yml b/tests/modules/spades/test.yml
index a400e79d..98bc9c8c 100644
--- a/tests/modules/spades/test.yml
+++ b/tests/modules/spades/test.yml
@@ -1,5 +1,5 @@
- name: spades test_spades_single_end
- command: nextflow run tests/modules/spades -entry test_spades_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/spades -entry test_spades_single_end -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
tags:
- spades
files:
@@ -12,7 +12,7 @@
- path: output/spades/test.spades.log
- name: spades test_spades_paired_end
- command: nextflow run tests/modules/spades -entry test_spades_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/spades -entry test_spades_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
tags:
- spades
files:
@@ -24,7 +24,7 @@
- path: output/spades/warnings.log
- name: spades test_spades_illumina_nanopore
- command: nextflow run tests/modules/spades -entry test_spades_illumina_nanopore -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/spades -entry test_spades_illumina_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
tags:
- spades
files:
@@ -38,7 +38,7 @@
- path: output/spades/warnings.log
- name: spades test_spades_illumina_pacbio
- command: nextflow run tests/modules/spades -entry test_spades_illumina_pacbio -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/spades -entry test_spades_illumina_pacbio -c ./tests/config/nextflow.config -c ./tests/modules/spades/nextflow.config
tags:
- spades
files:
diff --git a/tests/modules/spatyper/main.nf b/tests/modules/spatyper/main.nf
index 65729cc0..655845c7 100644
--- a/tests/modules/spatyper/main.nf
+++ b/tests/modules/spatyper/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { SPATYPER } from '../../../modules/spatyper/main.nf' addParams( options: [:] )
-include { SPATYPER as SPATYPER_ENRICH } from '../../../modules/spatyper/main.nf' addParams( options: [args: '--do_enrich'] )
+include { SPATYPER } from '../../../modules/spatyper/main.nf'
+include { SPATYPER as SPATYPER_ENRICH } from '../../../modules/spatyper/main.nf'
workflow test_spatyper {
input = [ [ id:'test' ],
diff --git a/tests/modules/spatyper/nextflow.config b/tests/modules/spatyper/nextflow.config
new file mode 100644
index 00000000..ac90a452
--- /dev/null
+++ b/tests/modules/spatyper/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SPATYPER_ENRICH {
+ ext.args = '--do_enrich'
+ }
+
+}
diff --git a/tests/modules/spatyper/test.yml b/tests/modules/spatyper/test.yml
index 49516812..6e1f8144 100644
--- a/tests/modules/spatyper/test.yml
+++ b/tests/modules/spatyper/test.yml
@@ -1,5 +1,5 @@
- name: spatyper test_spatyper
- command: nextflow run tests/modules/spatyper -entry test_spatyper -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/spatyper -entry test_spatyper -c ./tests/config/nextflow.config -c ./tests/modules/spatyper/nextflow.config
tags:
- spatyper
files:
@@ -7,7 +7,7 @@
md5sum: a698352823875171696e5e7ed7015c13
- name: spatyper test_spatyper_enrich
- command: nextflow run tests/modules/spatyper -entry test_spatyper_enrich -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/spatyper -entry test_spatyper_enrich -c ./tests/config/nextflow.config -c ./tests/modules/spatyper/nextflow.config
tags:
- spatyper
files:
diff --git a/tests/modules/sratools/fasterqdump/main.nf b/tests/modules/sratools/fasterqdump/main.nf
index 1a0e0c7a..2f838fd2 100644
--- a/tests/modules/sratools/fasterqdump/main.nf
+++ b/tests/modules/sratools/fasterqdump/main.nf
@@ -3,7 +3,7 @@
nextflow.enable.dsl = 2
include { UNTAR } from '../../../../modules/untar/main.nf'
-include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf' addParams( options: [:] )
+include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/main.nf'
workflow test_sratools_fasterqdump_single_end {
diff --git a/tests/modules/sratools/fasterqdump/nextflow.config b/tests/modules/sratools/fasterqdump/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/sratools/fasterqdump/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/sratools/fasterqdump/test.yml b/tests/modules/sratools/fasterqdump/test.yml
index 7d022a0d..64cf2404 100644
--- a/tests/modules/sratools/fasterqdump/test.yml
+++ b/tests/modules/sratools/fasterqdump/test.yml
@@ -1,7 +1,8 @@
- name: sratools fasterqdump test_sratools_fasterqdump_single_end
- command: nextflow run tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
tags:
- - subworkflows/sra_fastq
+ - sratools
+ - sratools/fasterqdump
files:
- path: output/sratools/SRR13255544.fastq.gz
md5sum: 1054c7b71884acdb5eed8a378f18be82
@@ -9,9 +10,10 @@
md5sum: 466d05dafb2eec672150754168010b4d
- name: sratools fasterqdump test_sratools_fasterqdump_paired_end
- command: nextflow run tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/sratools/fasterqdump/nextflow.config
tags:
- - subworkflows/sra_fastq
+ - sratools
+ - sratools/fasterqdump
files:
- path: output/sratools/SRR11140744_1.fastq.gz
md5sum: 193809c784a4ea132ab2a253fa4f55b6
diff --git a/tests/modules/sratools/prefetch/main.nf b/tests/modules/sratools/prefetch/main.nf
index 99439a7f..aa6252a1 100644
--- a/tests/modules/sratools/prefetch/main.nf
+++ b/tests/modules/sratools/prefetch/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf' addParams( options: [:] )
+include { SRATOOLS_PREFETCH } from '../../../../modules/sratools/prefetch/main.nf'
workflow test_sratools_prefetch {
diff --git a/tests/modules/sratools/prefetch/nextflow.config b/tests/modules/sratools/prefetch/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/sratools/prefetch/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/sratools/prefetch/test.yml b/tests/modules/sratools/prefetch/test.yml
index c23db12a..a2efef77 100644
--- a/tests/modules/sratools/prefetch/test.yml
+++ b/tests/modules/sratools/prefetch/test.yml
@@ -1,5 +1,5 @@
- name: sratools prefetch test_sratools_prefetch
- command: nextflow run tests/modules/sratools/prefetch -entry test_sratools_prefetch -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/sratools/prefetch -entry test_sratools_prefetch -c ./tests/config/nextflow.config -c ./tests/modules/sratools/prefetch/nextflow.config
tags:
- sratools/prefetch
- sratools
diff --git a/tests/modules/staphopiasccmec/main.nf b/tests/modules/staphopiasccmec/main.nf
index ec1b48e4..8ea310ce 100644
--- a/tests/modules/staphopiasccmec/main.nf
+++ b/tests/modules/staphopiasccmec/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { STAPHOPIASCCMEC } from '../../../modules/staphopiasccmec/main.nf' addParams( options: [:] )
-include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../modules/staphopiasccmec/main.nf' addParams( options: [args: '--hamming'] )
+include { STAPHOPIASCCMEC } from '../../../modules/staphopiasccmec/main.nf'
+include { STAPHOPIASCCMEC as STAPHOPIASCCMEC_HAMMING } from '../../../modules/staphopiasccmec/main.nf'
workflow test_staphopiasccmec {
diff --git a/tests/modules/staphopiasccmec/nextflow.config b/tests/modules/staphopiasccmec/nextflow.config
new file mode 100644
index 00000000..7ee97c2f
--- /dev/null
+++ b/tests/modules/staphopiasccmec/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: STAPHOPIASCCMEC_HAMMING {
+ ext.args = '--hamming'
+ }
+
+}
diff --git a/tests/modules/staphopiasccmec/test.yml b/tests/modules/staphopiasccmec/test.yml
index aadfec3e..ac3f66da 100644
--- a/tests/modules/staphopiasccmec/test.yml
+++ b/tests/modules/staphopiasccmec/test.yml
@@ -1,5 +1,5 @@
- name: staphopiasccmec test_staphopiasccmec
- command: nextflow run tests/modules/staphopiasccmec -entry test_staphopiasccmec -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/staphopiasccmec -entry test_staphopiasccmec -c ./tests/config/nextflow.config -c ./tests/modules/staphopiasccmec/nextflow.config
tags:
- staphopiasccmec
files:
@@ -7,7 +7,7 @@
md5sum: e6460d4164f3af5b290c5ccdb11343bf
- name: staphopiasccmec test_staphopiasccmec_hamming
- command: nextflow run tests/modules/staphopiasccmec -entry test_staphopiasccmec_hamming -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/staphopiasccmec -entry test_staphopiasccmec_hamming -c ./tests/config/nextflow.config -c ./tests/modules/staphopiasccmec/nextflow.config
tags:
- staphopiasccmec
files:
diff --git a/tests/modules/star/align/main.nf b/tests/modules/star/align/main.nf
index d7a7ef96..bf305d54 100644
--- a/tests/modules/star/align/main.nf
+++ b/tests/modules/star/align/main.nf
@@ -2,51 +2,77 @@
nextflow.enable.dsl = 2
-include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [args: '--genomeSAindexNbases 9'])
-include { STAR_ALIGN } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat'], seq_platform: 'illumina')
-include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'], seq_platform: 'illumina')
-include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/star/align/main.nf' addParams( options: [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30'] )
+include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf'
+include { STAR_ALIGN } from '../../../../modules/star/align/main.nf'
+include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../../../modules/star/align/main.nf'
+include { STAR_ALIGN as STAR_FOR_STARFUSION } from '../../../../modules/star/align/main.nf'
workflow test_star_alignment_single_end {
- input = [ [ id:'test', single_end:true ], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ]
+ ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+ star_ignore_sjdbgtf = false
+ seq_platform = 'illumina'
+ seq_center = false
+
STAR_GENOMEGENERATE ( fasta, gtf )
- STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
+ STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
}
workflow test_star_alignment_paired_end {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+ star_ignore_sjdbgtf = false
+ seq_platform = 'illumina'
+ seq_center = false
+
STAR_GENOMEGENERATE ( fasta, gtf )
- STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf )
+ STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
}
workflow test_star_alignment_paired_end_for_fusion {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+ star_ignore_sjdbgtf = false
+ seq_platform = 'illumina'
+ seq_center = false
+
STAR_GENOMEGENERATE ( fasta, gtf )
- STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf )
+ STAR_FOR_ARRIBA ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
}
workflow test_star_alignment_paired_end_for_starfusion {
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ]
- ]
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
+ star_ignore_sjdbgtf = false
+ seq_platform = false
+ seq_center = false
+
STAR_GENOMEGENERATE ( fasta, gtf )
- STAR_FOR_STARFUSION ( input, STAR_GENOMEGENERATE.out.index, gtf )
+ STAR_FOR_STARFUSION ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
}
diff --git a/tests/modules/star/align/nextflow.config b/tests/modules/star/align/nextflow.config
new file mode 100644
index 00000000..751f7837
--- /dev/null
+++ b/tests/modules/star/align/nextflow.config
@@ -0,0 +1,21 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: STAR_GENOMEGENERATE {
+ ext.args = '--genomeSAindexNbases 9'
+ }
+
+ withName: STAR_ALIGN {
+ ext.args = '--readFilesCommand zcat'
+ }
+
+ withName: STAR_FOR_ARRIBA {
+ ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50'
+ }
+
+ withName: STAR_FOR_STARFUSION {
+ ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30'
+ }
+
+}
diff --git a/tests/modules/star/align/test.yml b/tests/modules/star/align/test.yml
index 47731c5c..af5bebe5 100644
--- a/tests/modules/star/align/test.yml
+++ b/tests/modules/star/align/test.yml
@@ -1,39 +1,39 @@
- name: star align test_star_alignment_single_end
- command: nextflow run tests/modules/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/star/align -entry test_star_alignment_single_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
tags:
- star/align
- star
files:
- - path: output/index/star/Genome
+ - path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/star/Log.out
- - path: output/index/star/SA
+ - path: output/star/star/Log.out
+ - path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/star/SAindex
+ - path: output/star/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- - path: output/index/star/chrLength.txt
+ - path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/star/chrName.txt
+ - path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/star/chrNameLength.txt
+ - path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/star/chrStart.txt
+ - path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/star/exonGeTrInfo.tab
+ - path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/star/exonInfo.tab
+ - path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/star/geneInfo.tab
+ - path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/star/genomeParameters.txt
+ - path: output/star/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- - path: output/index/star/sjdbInfo.txt
+ - path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/star/sjdbList.fromGTF.out.tab
+ - path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/star/sjdbList.out.tab
+ - path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/star/transcriptInfo.tab
+ - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
md5sum: b9f5e2f6a624b64c300fe25dc3ac801f
@@ -43,41 +43,41 @@
- path: output/star/test.SJ.out.tab
- name: star align test_star_alignment_paired_end
- command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
tags:
- star/align
- star
files:
- - path: output/index/star/Genome
+ - path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/star/Log.out
- - path: output/index/star/SA
+ - path: output/star/star/Log.out
+ - path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/star/SAindex
+ - path: output/star/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- - path: output/index/star/chrLength.txt
+ - path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/star/chrName.txt
+ - path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/star/chrNameLength.txt
+ - path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/star/chrStart.txt
+ - path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/star/exonGeTrInfo.tab
+ - path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/star/exonInfo.tab
+ - path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/star/geneInfo.tab
+ - path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/star/genomeParameters.txt
+ - path: output/star/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- - path: output/index/star/sjdbInfo.txt
+ - path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/star/sjdbList.fromGTF.out.tab
+ - path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/star/sjdbList.out.tab
+ - path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/star/transcriptInfo.tab
+ - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
md5sum: 38d08f0b944a2a1b981a250d675aa0d9
@@ -87,41 +87,41 @@
- path: output/star/test.SJ.out.tab
- name: star align test_star_alignment_paired_end_for_fusion
- command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_fusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
tags:
- star/align
- star
files:
- - path: output/index/star/Genome
+ - path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/star/Log.out
- - path: output/index/star/SA
+ - path: output/star/star/Log.out
+ - path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/star/SAindex
+ - path: output/star/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- - path: output/index/star/chrLength.txt
+ - path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/star/chrName.txt
+ - path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/star/chrNameLength.txt
+ - path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/star/chrStart.txt
+ - path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/star/exonGeTrInfo.tab
+ - path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/star/exonInfo.tab
+ - path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/star/geneInfo.tab
+ - path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/star/genomeParameters.txt
+ - path: output/star/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- - path: output/index/star/sjdbInfo.txt
+ - path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/star/sjdbList.fromGTF.out.tab
+ - path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/star/sjdbList.out.tab
+ - path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/star/transcriptInfo.tab
+ - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
md5sum: c740d5177067c1fcc48ab7a16cd639d7
@@ -131,41 +131,41 @@
- path: output/star/test.SJ.out.tab
- name: star align test_star_alignment_paired_end_for_starfusion
- command: nextflow run tests/modules/star/align -entry test_star_alignment_paired_end_for_starfusion -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/star/align -entry test_star_alignment_paired_end_for_starfusion -c ./tests/config/nextflow.config -c ./tests/modules/star/align/nextflow.config
tags:
- star/align
- star
files:
- - path: output/index/star/Genome
+ - path: output/star/star/Genome
md5sum: a654229fbca6071dcb6b01ce7df704da
- - path: output/index/star/Log.out
- - path: output/index/star/SA
+ - path: output/star/star/Log.out
+ - path: output/star/star/SA
md5sum: 8c3edc46697b72c9e92440d4cf43506c
- - path: output/index/star/SAindex
+ - path: output/star/star/SAindex
md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
- - path: output/index/star/chrLength.txt
+ - path: output/star/star/chrLength.txt
md5sum: c81f40f27e72606d7d07097c1d56a5b5
- - path: output/index/star/chrName.txt
+ - path: output/star/star/chrName.txt
md5sum: 5ae68a67b70976ee95342a7451cb5af1
- - path: output/index/star/chrNameLength.txt
+ - path: output/star/star/chrNameLength.txt
md5sum: b190587cae0531f3cf25552d8aa674db
- - path: output/index/star/chrStart.txt
+ - path: output/star/star/chrStart.txt
md5sum: 8d3291e6bcdbe9902fbd7c887494173f
- - path: output/index/star/exonGeTrInfo.tab
+ - path: output/star/star/exonGeTrInfo.tab
md5sum: d04497f69d6ef889efd4d34fe63edcc4
- - path: output/index/star/exonInfo.tab
+ - path: output/star/star/exonInfo.tab
md5sum: 0d560290fab688b7268d88d5494bf9fe
- - path: output/index/star/geneInfo.tab
+ - path: output/star/star/geneInfo.tab
md5sum: 8b608537307443ffaee4927d2b428805
- - path: output/index/star/genomeParameters.txt
+ - path: output/star/star/genomeParameters.txt
md5sum: 3097677f4d8b2cb66770b9e55d343a7f
- - path: output/index/star/sjdbInfo.txt
+ - path: output/star/star/sjdbInfo.txt
md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
- - path: output/index/star/sjdbList.fromGTF.out.tab
+ - path: output/star/star/sjdbList.fromGTF.out.tab
md5sum: 8760c33e966dad0b39f440301ebbdee4
- - path: output/index/star/sjdbList.out.tab
+ - path: output/star/star/sjdbList.out.tab
md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1
- - path: output/index/star/transcriptInfo.tab
+ - path: output/star/star/transcriptInfo.tab
md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
- path: output/star/test.Aligned.out.bam
md5sum: a1bd1b40950a58ea2776908076160052
diff --git a/tests/modules/star/genomegenerate/main.nf b/tests/modules/star/genomegenerate/main.nf
index 7f9e3072..31601478 100644
--- a/tests/modules/star/genomegenerate/main.nf
+++ b/tests/modules/star/genomegenerate/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf' addParams( options: [publish_dir:'star'] )
+include { STAR_GENOMEGENERATE } from '../../../../modules/star/genomegenerate/main.nf'
workflow test_star_genomegenerate {
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/star/genomegenerate/nextflow.config b/tests/modules/star/genomegenerate/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/star/genomegenerate/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/star/genomegenerate/test.yml b/tests/modules/star/genomegenerate/test.yml
index df8d5efc..0e397009 100644
--- a/tests/modules/star/genomegenerate/test.yml
+++ b/tests/modules/star/genomegenerate/test.yml
@@ -1,5 +1,5 @@
- name: star genomegenerate test_star_genomegenerate
- command: nextflow run tests/modules/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/star/genomegenerate -entry test_star_genomegenerate -c ./tests/config/nextflow.config -c ./tests/modules/star/genomegenerate/nextflow.config
tags:
- star
- star/genomegenerate
diff --git a/tests/modules/strelka/germline/main.nf b/tests/modules/strelka/germline/main.nf
index 0d5193bb..c50d76e1 100644
--- a/tests/modules/strelka/germline/main.nf
+++ b/tests/modules/strelka/germline/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf' addParams( options: [:] )
+include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf'
workflow test_strelka_germline {
input = [
diff --git a/tests/modules/strelka/germline/nextflow.config b/tests/modules/strelka/germline/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/strelka/germline/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/strelka/germline/test.yml b/tests/modules/strelka/germline/test.yml
index a3ab3ef6..8db81aa0 100644
--- a/tests/modules/strelka/germline/test.yml
+++ b/tests/modules/strelka/germline/test.yml
@@ -1,5 +1,5 @@
- name: strelka germline test_strelka_germline
- command: nextflow run tests/modules/strelka/germline -entry test_strelka_germline -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline -c ./tests/config/nextflow.config -c ./tests/modules/strelka/germline/nextflow.config
tags:
- strelka
- strelka/germline
@@ -10,7 +10,7 @@
- path: output/strelka/test.variants.vcf.gz.tbi
- name: strelka germline test_strelka_germline_target_bed
- command: nextflow run tests/modules/strelka/germline -entry test_strelka_germline_target_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/strelka/germline -entry test_strelka_germline_target_bed -c ./tests/config/nextflow.config -c ./tests/modules/strelka/germline/nextflow.config
tags:
- strelka
- strelka/germline
diff --git a/tests/modules/strelka/somatic/main.nf b/tests/modules/strelka/somatic/main.nf
index 60127f58..b1d4efeb 100644
--- a/tests/modules/strelka/somatic/main.nf
+++ b/tests/modules/strelka/somatic/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { STRELKA_SOMATIC } from '../../../../modules/strelka/somatic/main.nf' addParams( options: [:] )
+include { STRELKA_SOMATIC } from '../../../../modules/strelka/somatic/main.nf'
workflow test_strelka_somatic {
diff --git a/tests/modules/strelka/somatic/nextflow.config b/tests/modules/strelka/somatic/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/strelka/somatic/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/strelka/somatic/test.yml b/tests/modules/strelka/somatic/test.yml
index b461d335..a56f955a 100644
--- a/tests/modules/strelka/somatic/test.yml
+++ b/tests/modules/strelka/somatic/test.yml
@@ -1,5 +1,5 @@
- name: strelka somatic test_strelka_somatic
- command: nextflow run tests/modules/strelka/somatic -entry test_strelka_somatic -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config
tags:
- strelka
- strelka/somatic
@@ -12,7 +12,7 @@
md5sum: 4cb176febbc8c26d717a6c6e67b9c905
- name: strelka somatic test_strelka__best_practices_somatic
- command: nextflow run tests/modules/strelka/somatic -entry test_strelka__best_practices_somatic -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka__best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config
tags:
- strelka
- strelka/somatic
diff --git a/tests/modules/stringtie/merge/main.nf b/tests/modules/stringtie/merge/main.nf
index 49ff5a41..7851e755 100644
--- a/tests/modules/stringtie/merge/main.nf
+++ b/tests/modules/stringtie/merge/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
-include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf' addParams( options: [:] )
+include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
/*
* Test with forward strandedness
diff --git a/tests/modules/stringtie/merge/nextflow.config b/tests/modules/stringtie/merge/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/stringtie/merge/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/stringtie/merge/test.yml b/tests/modules/stringtie/merge/test.yml
index e6436612..392a1d7c 100644
--- a/tests/modules/stringtie/merge/test.yml
+++ b/tests/modules/stringtie/merge/test.yml
@@ -1,5 +1,5 @@
- name: stringtie merge forward-strand
- command: nextflow run tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
tags:
- stringtie
- stringtie/merge
@@ -24,7 +24,7 @@
md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
- name: stringtie merge test_stringtie_reverse_merge
- command: nextflow run tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
tags:
- stringtie
- stringtie/merge
diff --git a/tests/modules/stringtie/stringtie/main.nf b/tests/modules/stringtie/stringtie/main.nf
index b902cc41..ae6abe67 100644
--- a/tests/modules/stringtie/stringtie/main.nf
+++ b/tests/modules/stringtie/stringtie/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf' addParams( options: [:] )
+include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
//
// Test with forward strandedness
//
diff --git a/tests/modules/stringtie/stringtie/nextflow.config b/tests/modules/stringtie/stringtie/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/stringtie/stringtie/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/stringtie/stringtie/test.yml b/tests/modules/stringtie/stringtie/test.yml
index 28c1b3c2..732b9fd1 100644
--- a/tests/modules/stringtie/stringtie/test.yml
+++ b/tests/modules/stringtie/stringtie/test.yml
@@ -1,5 +1,5 @@
- name: stringtie stringtie forward
- command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_forward -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config
tags:
- stringtie
- stringtie/stringtie
@@ -21,7 +21,7 @@
md5sum: e981c0038295ae54b63cedb1083f1540
- name: stringtie stringtie reverse
- command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/stringtie/stringtie/ -entry test_stringtie_reverse -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/stringtie/nextflow.config
tags:
- stringtie
- stringtie/stringtie
diff --git a/tests/modules/subread/featurecounts/main.nf b/tests/modules/subread/featurecounts/main.nf
index eae60f80..a8fa5c75 100644
--- a/tests/modules/subread/featurecounts/main.nf
+++ b/tests/modules/subread/featurecounts/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { SUBREAD_FEATURECOUNTS } from '../../../../modules/subread/featurecounts/main.nf' addParams( options: [args:'-t CDS'] )
+include { SUBREAD_FEATURECOUNTS } from '../../../../modules/subread/featurecounts/main.nf'
workflow test_subread_featurecounts_forward {
diff --git a/tests/modules/subread/featurecounts/nextflow.config b/tests/modules/subread/featurecounts/nextflow.config
new file mode 100644
index 00000000..d9fd4fd5
--- /dev/null
+++ b/tests/modules/subread/featurecounts/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: SUBREAD_FEATURECOUNTS {
+ ext.args = '-t CDS'
+ }
+
+}
diff --git a/tests/modules/subread/featurecounts/test.yml b/tests/modules/subread/featurecounts/test.yml
index be6bed47..7cc24457 100644
--- a/tests/modules/subread/featurecounts/test.yml
+++ b/tests/modules/subread/featurecounts/test.yml
@@ -1,5 +1,5 @@
- name: subread featurecounts test_subread_featurecounts_forward
- command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_forward -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_forward -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config
tags:
- subread
- subread/featurecounts
@@ -10,7 +10,7 @@
md5sum: 8f602ff9a8ef467af43294e80b367cdf
- name: subread featurecounts test_subread_featurecounts_reverse
- command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config
tags:
- subread
- subread/featurecounts
@@ -21,7 +21,7 @@
md5sum: 7cfa30ad678b9bc1bc63afbb0281547b
- name: subread featurecounts test_subread_featurecounts_unstranded
- command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c ./tests/config/nextflow.config -c ./tests/modules/subread/featurecounts/nextflow.config
tags:
- subread
- subread/featurecounts
diff --git a/tests/modules/tabix/bgzip/main.nf b/tests/modules/tabix/bgzip/main.nf
index 8756b17d..4d349890 100644
--- a/tests/modules/tabix/bgzip/main.nf
+++ b/tests/modules/tabix/bgzip/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { TABIX_BGZIP } from '../../../../modules/tabix/bgzip/main.nf' addParams( options: [:] )
+include { TABIX_BGZIP } from '../../../../modules/tabix/bgzip/main.nf'
workflow test_tabix_bgzip {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/tabix/bgzip/nextflow.config b/tests/modules/tabix/bgzip/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/tabix/bgzip/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/tabix/bgzip/test.yml b/tests/modules/tabix/bgzip/test.yml
index 58412979..19357655 100644
--- a/tests/modules/tabix/bgzip/test.yml
+++ b/tests/modules/tabix/bgzip/test.yml
@@ -1,5 +1,5 @@
- name: tabix bgzip
- command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tabix/bgzip -entry test_tabix_bgzip -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgzip/nextflow.config
tags:
- tabix
- tabix/bgzip
diff --git a/tests/modules/tabix/bgziptabix/main.nf b/tests/modules/tabix/bgziptabix/main.nf
index 51e242fd..b2ff70d0 100644
--- a/tests/modules/tabix/bgziptabix/main.nf
+++ b/tests/modules/tabix/bgziptabix/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main.nf' addParams( options: ['args2': '-p vcf'] )
+include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main.nf'
workflow test_tabix_bgziptabix {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/tabix/bgziptabix/nextflow.config b/tests/modules/tabix/bgziptabix/nextflow.config
new file mode 100644
index 00000000..041bfa6a
--- /dev/null
+++ b/tests/modules/tabix/bgziptabix/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: TABIX_BGZIPTABIX {
+ ext.args2 = '-p vcf'
+ }
+
+}
diff --git a/tests/modules/tabix/bgziptabix/test.yml b/tests/modules/tabix/bgziptabix/test.yml
index 31048109..1bcfa88a 100644
--- a/tests/modules/tabix/bgziptabix/test.yml
+++ b/tests/modules/tabix/bgziptabix/test.yml
@@ -1,5 +1,5 @@
- name: tabix bgziptabix
- command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgziptabix/nextflow.config
tags:
- tabix
- tabix/bgziptabix
diff --git a/tests/modules/tabix/tabix/main.nf b/tests/modules/tabix/tabix/main.nf
index 0963ffcd..993ee812 100644
--- a/tests/modules/tabix/tabix/main.nf
+++ b/tests/modules/tabix/tabix/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf' addParams( options: ['args': '-p bed'] )
-include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf' addParams( options: ['args': '-p gff'] )
-include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf' addParams( options: ['args': '-p vcf'] )
+include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf'
workflow test_tabix_tabix_bed {
input = [ [ id:'B.bed' ], // meta map
diff --git a/tests/modules/tabix/tabix/nextflow.config b/tests/modules/tabix/tabix/nextflow.config
new file mode 100644
index 00000000..aa97a873
--- /dev/null
+++ b/tests/modules/tabix/tabix/nextflow.config
@@ -0,0 +1,17 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: TABIX_BED {
+ ext.args = '-p bed'
+ }
+
+ withName: TABIX_GFF {
+ ext.args = '-p gff'
+ }
+
+ withName: TABIX_VCF {
+ ext.args = '-p vcf'
+ }
+
+}
diff --git a/tests/modules/tabix/tabix/test.yml b/tests/modules/tabix/tabix/test.yml
index 646215c8..46be28dd 100644
--- a/tests/modules/tabix/tabix/test.yml
+++ b/tests/modules/tabix/tabix/test.yml
@@ -1,5 +1,5 @@
- name: tabix tabix bed
- command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_bed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_bed -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
tags:
- tabix
- tabix/tabix
@@ -7,7 +7,7 @@
- path: ./output/tabix/test.bed.gz.tbi
md5sum: 5b40851ab6b8ccf7946313c86481c0df
- name: tabix tabix gff
- command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_gff -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
tags:
- tabix
- tabix/tabix
@@ -15,7 +15,7 @@
- path: ./output/tabix/genome.gff3.gz.tbi
md5sum: f79a67d95a98076e04fbe0455d825926
- name: tabix tabix vcf
- command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
tags:
- tabix
- tabix/tabix
diff --git a/tests/modules/tbprofiler/profile/main.nf b/tests/modules/tbprofiler/profile/main.nf
index e0c6ef56..0141a77f 100644
--- a/tests/modules/tbprofiler/profile/main.nf
+++ b/tests/modules/tbprofiler/profile/main.nf
@@ -2,23 +2,27 @@
nextflow.enable.dsl = 2
-include { TBPROFILER_PROFILE as TBPROFILER_PROFILE_ILLUMINA } from '../../../../modules/tbprofiler/profile/main.nf' addParams( options: [args: '--platform illumina'] )
-include { TBPROFILER_PROFILE as TBPROFILER_PROFILE_NANOPORE} from '../../../../modules/tbprofiler/profile/main.nf' addParams( options: [args: '--platform nanopore'] )
+include { TBPROFILER_PROFILE } from '../../../../modules/tbprofiler/profile/main.nf'
workflow test_tbprofiler_profile_illumina {
-
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
- TBPROFILER_PROFILE_ILLUMINA ( input )
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
+
+ TBPROFILER_PROFILE ( input )
}
-
workflow test_tbprofiler_profile_nanopore {
-
- input = [ [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
- TBPROFILER_PROFILE_NANOPORE ( input )
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+ ]
+
+ TBPROFILER_PROFILE ( input )
}
diff --git a/tests/modules/tbprofiler/profile/nextflow.config b/tests/modules/tbprofiler/profile/nextflow.config
new file mode 100644
index 00000000..50cb99c6
--- /dev/null
+++ b/tests/modules/tbprofiler/profile/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: TBPROFILER_PROFILE_ILLUMINA {
+ ext.args = '--platform illumina'
+ }
+
+ withName: TBPROFILER_PROFILE_NANOPORE {
+ ext.args = '--platform nanopore'
+ }
+
+}
diff --git a/tests/modules/tbprofiler/profile/test.yml b/tests/modules/tbprofiler/profile/test.yml
index abfb552d..8b40f1fa 100644
--- a/tests/modules/tbprofiler/profile/test.yml
+++ b/tests/modules/tbprofiler/profile/test.yml
@@ -1,5 +1,5 @@
- name: tbprofiler profile illumina
- command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_illumina -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config
tags:
- tbprofiler
- tbprofiler/profile
@@ -10,7 +10,7 @@
- path: output/tbprofiler/vcf/test.targets.csq.vcf.gz
- name: tbprofiler profile nanopore
- command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tbprofiler/profile -entry test_tbprofiler_profile_nanopore -c ./tests/config/nextflow.config -c ./tests/modules/tbprofiler/profile/nextflow.config
tags:
- tbprofiler
- tbprofiler/profile
diff --git a/tests/modules/tiddit/cov/main.nf b/tests/modules/tiddit/cov/main.nf
index aed3516c..1bb35145 100644
--- a/tests/modules/tiddit/cov/main.nf
+++ b/tests/modules/tiddit/cov/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { TIDDIT_COV } from '../../../../modules/tiddit/cov/main.nf' addParams( options: [:] )
+include { TIDDIT_COV } from '../../../../modules/tiddit/cov/main.nf'
workflow test_tiddit_cov {
diff --git a/tests/modules/tiddit/cov/nextflow.config b/tests/modules/tiddit/cov/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/tiddit/cov/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/tiddit/cov/test.yml b/tests/modules/tiddit/cov/test.yml
index c2aa6439..90c4cbb3 100644
--- a/tests/modules/tiddit/cov/test.yml
+++ b/tests/modules/tiddit/cov/test.yml
@@ -1,5 +1,5 @@
- name: tiddit cov test_tiddit_cov
- command: nextflow run tests/modules/tiddit/cov -entry test_tiddit_cov -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
tags:
- tiddit
- tiddit/cov
@@ -8,7 +8,7 @@
md5sum: f7974948f809f94879d8a60b726194f5
- name: tiddit cov test_tiddit_cov_no_ref
- command: nextflow run tests/modules/tiddit/cov -entry test_tiddit_cov_no_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tiddit/cov -entry test_tiddit_cov_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/cov/nextflow.config
tags:
- tiddit
- tiddit/cov
diff --git a/tests/modules/tiddit/sv/main.nf b/tests/modules/tiddit/sv/main.nf
index 8a5a8140..8dae4950 100644
--- a/tests/modules/tiddit/sv/main.nf
+++ b/tests/modules/tiddit/sv/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf' addParams( options: [:] )
+include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
workflow test_tiddit_sv {
input = [
diff --git a/tests/modules/tiddit/sv/nextflow.config b/tests/modules/tiddit/sv/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/tiddit/sv/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/tiddit/sv/test.yml b/tests/modules/tiddit/sv/test.yml
index ed19bf14..168d21c5 100644
--- a/tests/modules/tiddit/sv/test.yml
+++ b/tests/modules/tiddit/sv/test.yml
@@ -1,5 +1,5 @@
- name: tiddit sv
- command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
tags:
- tiddit
- tiddit/sv
@@ -11,7 +11,7 @@
- path: output/tiddit/test.vcf
- name: tiddit sv no ref
- command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
tags:
- tiddit
- tiddit/sv
diff --git a/tests/modules/trimgalore/main.nf b/tests/modules/trimgalore/main.nf
index 3001469d..adeda539 100644
--- a/tests/modules/trimgalore/main.nf
+++ b/tests/modules/trimgalore/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { TRIMGALORE } from '../../../modules/trimgalore/main.nf' addParams( options: [:] )
+include { TRIMGALORE } from '../../../modules/trimgalore/main.nf'
//
// Test with single-end data
diff --git a/tests/modules/trimgalore/nextflow.config b/tests/modules/trimgalore/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/trimgalore/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/trimgalore/test.yml b/tests/modules/trimgalore/test.yml
index c176f592..ecbd2b5a 100644
--- a/tests/modules/trimgalore/test.yml
+++ b/tests/modules/trimgalore/test.yml
@@ -1,5 +1,5 @@
- name: trimgalore single-end
- command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimgalore/nextflow.config
tags:
- trimgalore
files:
@@ -9,7 +9,7 @@
- path: ./output/trimgalore/test_trimmed.fq.gz
- name: trimgalore paired-end
- command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/trimgalore/ -entry test_trimgalore_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimgalore/nextflow.config
tags:
- trimgalore
files:
diff --git a/tests/modules/ucsc/bed12tobigbed/main.nf b/tests/modules/ucsc/bed12tobigbed/main.nf
index 8ed64166..7590fc0e 100644
--- a/tests/modules/ucsc/bed12tobigbed/main.nf
+++ b/tests/modules/ucsc/bed12tobigbed/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UCSC_BED12TOBIGBED } from '../../../../modules/ucsc/bed12tobigbed/main.nf' addParams( options: [:] )
+include { UCSC_BED12TOBIGBED } from '../../../../modules/ucsc/bed12tobigbed/main.nf'
workflow test_ucsc_bed12tobigbed {
input = [ [ id: 'test' ], // meta map
diff --git a/tests/modules/ucsc/bed12tobigbed/nextflow.config b/tests/modules/ucsc/bed12tobigbed/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ucsc/bed12tobigbed/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ucsc/bed12tobigbed/test.yml b/tests/modules/ucsc/bed12tobigbed/test.yml
index e0ee6f75..6bd4262d 100644
--- a/tests/modules/ucsc/bed12tobigbed/test.yml
+++ b/tests/modules/ucsc/bed12tobigbed/test.yml
@@ -1,5 +1,5 @@
- name: ucsc bed12tobigbed
- command: nextflow run ./tests/modules/ucsc/bed12tobigbed -entry test_ucsc_bed12tobigbed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ucsc/bed12tobigbed -entry test_ucsc_bed12tobigbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bed12tobigbed/nextflow.config
tags:
- ucsc/bed12tobigbed
files:
diff --git a/tests/modules/ucsc/bedclip/main.nf b/tests/modules/ucsc/bedclip/main.nf
index 162c2eb4..8ccfd3b0 100755
--- a/tests/modules/ucsc/bedclip/main.nf
+++ b/tests/modules/ucsc/bedclip/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UCSC_BEDCLIP } from '../../../../modules/ucsc/bedclip/main.nf' addParams( options: [suffix:'.clip'] )
+include { UCSC_BEDCLIP } from '../../../../modules/ucsc/bedclip/main.nf'
workflow test_ucsc_bedclip {
input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/ucsc/bedclip/nextflow.config b/tests/modules/ucsc/bedclip/nextflow.config
new file mode 100644
index 00000000..4adc3b8f
--- /dev/null
+++ b/tests/modules/ucsc/bedclip/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: UCSC_BEDCLIP {
+ ext.suffix = '.clip'
+ }
+
+}
diff --git a/tests/modules/ucsc/bedclip/test.yml b/tests/modules/ucsc/bedclip/test.yml
index 103795da..bcf22c71 100755
--- a/tests/modules/ucsc/bedclip/test.yml
+++ b/tests/modules/ucsc/bedclip/test.yml
@@ -1,5 +1,5 @@
- name: ucsc bedclip
- command: nextflow run ./tests/modules/ucsc/bedclip -entry test_ucsc_bedclip -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ucsc/bedclip -entry test_ucsc_bedclip -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedclip/nextflow.config
tags:
- ucsc
- ucsc/bedclip
diff --git a/tests/modules/ucsc/bedgraphtobigwig/main.nf b/tests/modules/ucsc/bedgraphtobigwig/main.nf
index 8d83e235..c6db7225 100644
--- a/tests/modules/ucsc/bedgraphtobigwig/main.nf
+++ b/tests/modules/ucsc/bedgraphtobigwig/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../modules/ucsc/bedgraphtobigwig/main.nf' addParams( options: [:] )
+include { UCSC_BEDGRAPHTOBIGWIG } from '../../../../modules/ucsc/bedgraphtobigwig/main.nf'
workflow test_ucsc_bedgraphtobigwig {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/ucsc/bedgraphtobigwig/nextflow.config b/tests/modules/ucsc/bedgraphtobigwig/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ucsc/bedgraphtobigwig/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ucsc/bedgraphtobigwig/test.yml b/tests/modules/ucsc/bedgraphtobigwig/test.yml
index 726a07ca..c00a0231 100644
--- a/tests/modules/ucsc/bedgraphtobigwig/test.yml
+++ b/tests/modules/ucsc/bedgraphtobigwig/test.yml
@@ -1,5 +1,5 @@
- name: ucsc bedgraphtobigwig
- command: nextflow run ./tests/modules/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bedgraphtobigwig/nextflow.config
tags:
- ucsc/bedgraphtobigwig
files:
diff --git a/tests/modules/ucsc/bigwigaverageoverbed/main.nf b/tests/modules/ucsc/bigwigaverageoverbed/main.nf
index 9bd5a5e2..3b20dc32 100644
--- a/tests/modules/ucsc/bigwigaverageoverbed/main.nf
+++ b/tests/modules/ucsc/bigwigaverageoverbed/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/ucsc/bigwigaverageoverbed/main.nf' addParams( options: [:] )
+include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../modules/ucsc/bigwigaverageoverbed/main.nf'
workflow test_ucsc_bigwigaverageoverbed {
input = [
diff --git a/tests/modules/ucsc/bigwigaverageoverbed/nextflow.config b/tests/modules/ucsc/bigwigaverageoverbed/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ucsc/bigwigaverageoverbed/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ucsc/bigwigaverageoverbed/test.yml b/tests/modules/ucsc/bigwigaverageoverbed/test.yml
index 641e9be5..7344c944 100644
--- a/tests/modules/ucsc/bigwigaverageoverbed/test.yml
+++ b/tests/modules/ucsc/bigwigaverageoverbed/test.yml
@@ -1,5 +1,5 @@
- name: ucsc bigwigaverageoverbed test_ucsc_bigwigaverageoverbed
- command: nextflow run tests/modules/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/bigwigaverageoverbed/nextflow.config
tags:
- ucsc
- ucsc/bigwigaverageoverbed
diff --git a/tests/modules/ucsc/liftover/main.nf b/tests/modules/ucsc/liftover/main.nf
index 9670759a..168193f4 100644
--- a/tests/modules/ucsc/liftover/main.nf
+++ b/tests/modules/ucsc/liftover/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UCSC_LIFTOVER } from '../../../../modules/ucsc/liftover/main.nf' addParams( options: [:] )
+include { UCSC_LIFTOVER } from '../../../../modules/ucsc/liftover/main.nf'
workflow test_ucsc_liftover {
diff --git a/tests/modules/ucsc/liftover/nextflow.config b/tests/modules/ucsc/liftover/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ucsc/liftover/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ucsc/liftover/test.yml b/tests/modules/ucsc/liftover/test.yml
index 74df6512..c3016189 100644
--- a/tests/modules/ucsc/liftover/test.yml
+++ b/tests/modules/ucsc/liftover/test.yml
@@ -1,5 +1,5 @@
- name: ucsc liftover test_ucsc_liftover
- command: nextflow run tests/modules/ucsc/liftover -entry test_ucsc_liftover -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ucsc/liftover -entry test_ucsc_liftover -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/liftover/nextflow.config
tags:
- ucsc
- ucsc/liftover
diff --git a/tests/modules/ucsc/wigtobigwig/main.nf b/tests/modules/ucsc/wigtobigwig/main.nf
index 81296ac4..614d4150 100644
--- a/tests/modules/ucsc/wigtobigwig/main.nf
+++ b/tests/modules/ucsc/wigtobigwig/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UCSC_WIGTOBIGWIG } from '../../../../modules/ucsc/wigtobigwig/main.nf' addParams( options: [:] )
+include { UCSC_WIGTOBIGWIG } from '../../../../modules/ucsc/wigtobigwig/main.nf'
workflow test_ucsc_wigtobigwig {
diff --git a/tests/modules/ucsc/wigtobigwig/nextflow.config b/tests/modules/ucsc/wigtobigwig/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/ucsc/wigtobigwig/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/ucsc/wigtobigwig/test.yml b/tests/modules/ucsc/wigtobigwig/test.yml
index 15388adb..08d4bce4 100644
--- a/tests/modules/ucsc/wigtobigwig/test.yml
+++ b/tests/modules/ucsc/wigtobigwig/test.yml
@@ -1,5 +1,5 @@
- name: ucsc wigtobigwig test_ucsc_wigtobigwig
- command: nextflow run tests/modules/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c ./tests/config/nextflow.config -c ./tests/modules/ucsc/wigtobigwig/nextflow.config
tags:
- ucsc
- ucsc/wigtobigwig
diff --git a/tests/modules/ultra/pipeline/main.nf b/tests/modules/ultra/pipeline/main.nf
index 1404712b..483d48fc 100644
--- a/tests/modules/ultra/pipeline/main.nf
+++ b/tests/modules/ultra/pipeline/main.nf
@@ -2,9 +2,9 @@
nextflow.enable.dsl = 2
-include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf' addParams( options: [:] )
-include { GUNZIP } from '../../../../modules/gunzip/main.nf' addParams( options: [:] )
-include { GFFREAD } from '../../../../modules/gffread/main.nf' addParams( options: [args: "--sort-alpha --keep-genes -T", suffix: "_sorted"] )
+include { ULTRA_PIPELINE } from '../../../../modules/ultra/pipeline/main.nf'
+include { GUNZIP } from '../../../../modules/gunzip/main.nf'
+include { GFFREAD } from '../../../../modules/gffread/main.nf'
workflow test_ultra_pipeline {
diff --git a/tests/modules/ultra/pipeline/nextflow.config b/tests/modules/ultra/pipeline/nextflow.config
new file mode 100644
index 00000000..a3b88ea3
--- /dev/null
+++ b/tests/modules/ultra/pipeline/nextflow.config
@@ -0,0 +1,10 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: GFFREAD {
+ ext.args = '--sort-alpha --keep-genes -T'
+ ext.suffix = '_sorted'
+ }
+
+}
diff --git a/tests/modules/ultra/pipeline/test.yml b/tests/modules/ultra/pipeline/test.yml
index 7140193b..d424ba73 100644
--- a/tests/modules/ultra/pipeline/test.yml
+++ b/tests/modules/ultra/pipeline/test.yml
@@ -1,5 +1,5 @@
- name: ultra pipeline test_ultra_pipeline
- command: nextflow run tests/modules/ultra/pipeline -entry test_ultra_pipeline -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/ultra/pipeline -entry test_ultra_pipeline -c ./tests/config/nextflow.config -c ./tests/modules/ultra/pipeline/nextflow.config
tags:
- ultra
- ultra/pipeline
diff --git a/tests/modules/unicycler/main.nf b/tests/modules/unicycler/main.nf
index 5352fc8b..861b139b 100644
--- a/tests/modules/unicycler/main.nf
+++ b/tests/modules/unicycler/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UNICYCLER } from '../../../modules/unicycler/main.nf' addParams( options: [:] )
+include { UNICYCLER } from '../../../modules/unicycler/main.nf'
workflow test_unicycler_single_end {
input = [ [ id:'test', single_end:true ], // meta map
diff --git a/tests/modules/unicycler/nextflow.config b/tests/modules/unicycler/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/unicycler/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/unicycler/test.yml b/tests/modules/unicycler/test.yml
index 124ac3e2..e25845aa 100644
--- a/tests/modules/unicycler/test.yml
+++ b/tests/modules/unicycler/test.yml
@@ -1,5 +1,5 @@
- name: unicycler test_unicycler_single_end
- command: nextflow run tests/modules/unicycler -entry test_unicycler_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/unicycler -entry test_unicycler_single_end -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config
tags:
- unicycler
files:
@@ -10,7 +10,7 @@
- "Assembly complete"
- name: unicycler test_unicycler_paired_end
- command: nextflow run tests/modules/unicycler -entry test_unicycler_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/unicycler -entry test_unicycler_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config
tags:
- unicycler
files:
@@ -21,7 +21,7 @@
- "Assembly complete"
- name: unicycler test_unicycler_shortreads_longreads
- command: nextflow run tests/modules/unicycler -entry test_unicycler_shortreads_longreads -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/unicycler -entry test_unicycler_shortreads_longreads -c ./tests/config/nextflow.config -c ./tests/modules/unicycler/nextflow.config
tags:
- unicycler
files:
diff --git a/tests/modules/untar/main.nf b/tests/modules/untar/main.nf
index b7317bd9..056e3ea7 100644
--- a/tests/modules/untar/main.nf
+++ b/tests/modules/untar/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UNTAR } from '../../../modules/untar/main.nf' addParams( options: [:] )
+include { UNTAR } from '../../../modules/untar/main.nf'
workflow test_untar {
input = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
diff --git a/tests/modules/untar/nextflow.config b/tests/modules/untar/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/untar/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/untar/test.yml b/tests/modules/untar/test.yml
index 9f48e86c..6d0d1d12 100644
--- a/tests/modules/untar/test.yml
+++ b/tests/modules/untar/test.yml
@@ -1,5 +1,5 @@
- name: untar
- command: nextflow run ./tests/modules/untar -entry test_untar -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
tags:
- untar
files:
diff --git a/tests/modules/unzip/main.nf b/tests/modules/unzip/main.nf
index b5b208be..520fe31e 100644
--- a/tests/modules/unzip/main.nf
+++ b/tests/modules/unzip/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { UNZIP } from '../../../modules/unzip/main.nf' addParams( options: [:] )
+include { UNZIP } from '../../../modules/unzip/main.nf'
workflow test_unzip {
diff --git a/tests/modules/unzip/nextflow.config b/tests/modules/unzip/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/unzip/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/unzip/test.yml b/tests/modules/unzip/test.yml
index 1b0b1a97..8016b4fa 100644
--- a/tests/modules/unzip/test.yml
+++ b/tests/modules/unzip/test.yml
@@ -1,5 +1,5 @@
- name: unzip
- command: nextflow run ./tests/modules/unzip -entry test_unzip -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/unzip -entry test_unzip -c ./tests/config/nextflow.config -c ./tests/modules/unzip/nextflow.config
tags:
- unzip
files:
diff --git a/tests/modules/variantbam/main.nf b/tests/modules/variantbam/main.nf
index 3ea09197..016a9104 100644
--- a/tests/modules/variantbam/main.nf
+++ b/tests/modules/variantbam/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { VARIANTBAM } from '../../../modules/variantbam/main.nf' addParams( options: [args: '-m 1'] )
+include { VARIANTBAM } from '../../../modules/variantbam/main.nf'
workflow test_variantbam {
diff --git a/tests/modules/variantbam/nextflow.config b/tests/modules/variantbam/nextflow.config
new file mode 100644
index 00000000..d0314010
--- /dev/null
+++ b/tests/modules/variantbam/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: VARIANTBAM {
+ ext.args = '-m 1'
+ }
+
+}
diff --git a/tests/modules/variantbam/test.yml b/tests/modules/variantbam/test.yml
index 51b824cd..1c9550ed 100644
--- a/tests/modules/variantbam/test.yml
+++ b/tests/modules/variantbam/test.yml
@@ -1,5 +1,5 @@
- name: variantbam test_variantbam
- command: nextflow run tests/modules/variantbam -entry test_variantbam -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/variantbam -entry test_variantbam -c ./tests/config/nextflow.config -c ./tests/modules/variantbam/nextflow.config
tags:
- variantbam
files:
diff --git a/tests/modules/vcftools/main.nf b/tests/modules/vcftools/main.nf
index 2d4997de..21f9aa88 100644
--- a/tests/modules/vcftools/main.nf
+++ b/tests/modules/vcftools/main.nf
@@ -2,8 +2,8 @@
nextflow.enable.dsl = 2
-include { VCFTOOLS as VCFTOOLS_BASE } from '../../../modules/vcftools/main.nf' addParams( options: ['args': '--freq'] )
-include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/vcftools/main.nf' addParams( options: ['args': '--freq --exclude-bed'] )
+include { VCFTOOLS as VCFTOOLS_BASE } from '../../../modules/vcftools/main.nf'
+include { VCFTOOLS as VCFTOOLS_OPTIONAL } from '../../../modules/vcftools/main.nf'
workflow test_vcftools_vcf_base {
input = [ [ id:'test' ], // meta map
diff --git a/tests/modules/vcftools/nextflow.config b/tests/modules/vcftools/nextflow.config
new file mode 100644
index 00000000..6865bbea
--- /dev/null
+++ b/tests/modules/vcftools/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: VCFTOOLS_BASE {
+ ext.args = '--freq'
+ }
+
+ withName: VCFTOOLS_OPTIONAL {
+ ext.args = '--freq --exclude-bed'
+ }
+
+}
diff --git a/tests/modules/vcftools/test.yml b/tests/modules/vcftools/test.yml
index 81529be2..5314ea75 100644
--- a/tests/modules/vcftools/test.yml
+++ b/tests/modules/vcftools/test.yml
@@ -1,5 +1,5 @@
- name: vcftools test_vcftools_vcf_base
- command: nextflow run tests/modules/vcftools -entry test_vcftools_vcf_base -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcf_base -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
tags:
- vcftools
files:
@@ -7,7 +7,7 @@
md5sum: 7f126655f17268fd1a338734f62868e9
- name: vcftools test_vcftools_vcfgz_base
- command: nextflow run tests/modules/vcftools -entry test_vcftools_vcfgz_base -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcfgz_base -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
tags:
- vcftools
files:
@@ -15,7 +15,7 @@
md5sum: 7f126655f17268fd1a338734f62868e9
- name: vcftools test_vcftools_vcf_optional
- command: nextflow run tests/modules/vcftools -entry test_vcftools_vcf_optional -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcf_optional -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
tags:
- vcftools
files:
@@ -23,7 +23,7 @@
md5sum: 7f126655f17268fd1a338734f62868e9
- name: vcftools test_vcftools_vcfgz_optional
- command: nextflow run tests/modules/vcftools -entry test_vcftools_vcfgz_optional -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/vcftools -entry test_vcftools_vcfgz_optional -c ./tests/config/nextflow.config -c ./tests/modules/vcftools/nextflow.config
tags:
- vcftools
files:
diff --git a/tests/modules/yara/index/main.nf b/tests/modules/yara/index/main.nf
index 35a86182..89eb0f7d 100644
--- a/tests/modules/yara/index/main.nf
+++ b/tests/modules/yara/index/main.nf
@@ -2,7 +2,7 @@
nextflow.enable.dsl = 2
-include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: [publish_dir:'yara'] )
+include { YARA_INDEX } from '../../../../modules/yara/index/main.nf'
workflow test_yara_index {
diff --git a/tests/modules/yara/index/nextflow.config b/tests/modules/yara/index/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/yara/index/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/yara/index/test.yml b/tests/modules/yara/index/test.yml
index de6f1cf6..a8d17866 100644
--- a/tests/modules/yara/index/test.yml
+++ b/tests/modules/yara/index/test.yml
@@ -1,5 +1,5 @@
- name: yara index test_yara_index
- command: nextflow run tests/modules/yara/index -entry test_yara_index -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/yara/index -entry test_yara_index -c ./tests/config/nextflow.config -c ./tests/modules/yara/index/nextflow.config
tags:
- yara/index
- yara
diff --git a/tests/modules/yara/mapper/main.nf b/tests/modules/yara/mapper/main.nf
index 9cdce40d..18800eb3 100644
--- a/tests/modules/yara/mapper/main.nf
+++ b/tests/modules/yara/mapper/main.nf
@@ -3,15 +3,18 @@
nextflow.enable.dsl = 2
-include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams(options: ['args': '-e 3'])
-include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf' addParams(options: ['args': '-e 3'])
+include { YARA_INDEX } from '../../../../modules/yara/index/main.nf'
+include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf'
workflow test_yara_single_end {
+ input = [
+ [ id:'test', single_end:true ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- input = [ [ id:'test', single_end:true ], // meta map
- file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-
YARA_INDEX ( fasta )
YARA_MAPPER ( input, YARA_INDEX.out.index )
@@ -19,12 +22,15 @@ workflow test_yara_single_end {
workflow test_yara_paired_end {
+ input = [
+ [ id:'test', single_end:false ], // meta map
+ [
+ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+ ]
+ ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
- input = [ [ id:'test', single_end:false ], // meta map
- [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
- file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
-
YARA_INDEX ( fasta )
YARA_MAPPER ( input, YARA_INDEX.out.index )
}
diff --git a/tests/modules/yara/mapper/nextflow.config b/tests/modules/yara/mapper/nextflow.config
new file mode 100644
index 00000000..a626a8fc
--- /dev/null
+++ b/tests/modules/yara/mapper/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+ withName: YARA_INDEX {
+ ext.args = '-e 3'
+ }
+
+ withName: YARA_MAPPER {
+ ext.args = '-e 3'
+ }
+
+}
diff --git a/tests/modules/yara/mapper/test.yml b/tests/modules/yara/mapper/test.yml
index 51b056df..186f70b4 100644
--- a/tests/modules/yara/mapper/test.yml
+++ b/tests/modules/yara/mapper/test.yml
@@ -1,68 +1,68 @@
- name: yara mapper test_yara_single_end
- command: nextflow run tests/modules/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/yara/mapper -entry test_yara_single_end -c ./tests/config/nextflow.config -c ./tests/modules/yara/mapper/nextflow.config
tags:
- yara/mapper
- yara
files:
- path: output/yara/test.mapped.bam
- - path: output/index/yara/yara.txt.size
+ - path: output/yara/yara/yara.txt.size
md5sum: 063987b3c3f747be7d2b8043c9d91000
- - path: output/index/yara/yara.lf.drs
+ - path: output/yara/yara/yara.lf.drs
md5sum: 55a54008ad1ba589aa210d2629c1df41
- - path: output/index/yara/yara.lf.pst
+ - path: output/yara/yara/yara.lf.pst
md5sum: e8daba34298e99e42942435286f9b3f0
- - path: output/index/yara/yara.sa.len
+ - path: output/yara/yara/yara.sa.len
md5sum: 45677f66c28c79c02250ceb8b58645e8
- - path: output/index/yara/yara.rid.concat
+ - path: output/yara/yara/yara.rid.concat
md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
- - path: output/index/yara/yara.txt.concat
+ - path: output/yara/yara/yara.txt.concat
md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
- - path: output/index/yara/yara.sa.val
+ - path: output/yara/yara/yara.sa.val
md5sum: ce57cc82e2d3ae7b9824210f54168ce9
- - path: output/index/yara/yara.sa.ind
+ - path: output/yara/yara/yara.sa.ind
md5sum: 464314583efb5f07260b0efecc29a1ce
- - path: output/index/yara/yara.rid.limits
+ - path: output/yara/yara/yara.rid.limits
md5sum: 8b814661f30a0c9e350bfbcb454930ce
- - path: output/index/yara/yara.lf.drp
+ - path: output/yara/yara/yara.lf.drp
md5sum: 3ef99a87a4e44513f46d42f4261f7842
- - path: output/index/yara/yara.txt.limits
+ - path: output/yara/yara/yara.txt.limits
md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
- - path: output/index/yara/yara.lf.drv
+ - path: output/yara/yara/yara.lf.drv
md5sum: cf6408307fe9fd7f99c33f521bf95550
- - path: output/index/yara/yara.fasta
+ - path: output/yara/yara/yara.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6
- name: yara mapper test_yara_paired_end
- command: nextflow run tests/modules/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config
+ command: nextflow run ./tests/modules/yara/mapper -entry test_yara_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/yara/mapper/nextflow.config
tags:
- yara/mapper
- yara
files:
- path: output/yara/test_2.mapped.bam
- path: output/yara/test_1.mapped.bam
- - path: output/index/yara/yara.txt.size
+ - path: output/yara/yara/yara.txt.size
md5sum: 063987b3c3f747be7d2b8043c9d91000
- - path: output/index/yara/yara.lf.drs
+ - path: output/yara/yara/yara.lf.drs
md5sum: 55a54008ad1ba589aa210d2629c1df41
- - path: output/index/yara/yara.lf.pst
+ - path: output/yara/yara/yara.lf.pst
md5sum: e8daba34298e99e42942435286f9b3f0
- - path: output/index/yara/yara.sa.len
+ - path: output/yara/yara/yara.sa.len
md5sum: 45677f66c28c79c02250ceb8b58645e8
- - path: output/index/yara/yara.rid.concat
+ - path: output/yara/yara/yara.rid.concat
md5sum: 1e4e4c88ddeaf907a12f02f0d88367c5
- - path: output/index/yara/yara.txt.concat
+ - path: output/yara/yara/yara.txt.concat
md5sum: 6074d1933c9e7e5ab05fa0def5ce28c0
- - path: output/index/yara/yara.sa.val
+ - path: output/yara/yara/yara.sa.val
md5sum: ce57cc82e2d3ae7b9824210f54168ce9
- - path: output/index/yara/yara.sa.ind
+ - path: output/yara/yara/yara.sa.ind
md5sum: 464314583efb5f07260b0efecc29a1ce
- - path: output/index/yara/yara.rid.limits
+ - path: output/yara/yara/yara.rid.limits
md5sum: 8b814661f30a0c9e350bfbcb454930ce
- - path: output/index/yara/yara.lf.drp
+ - path: output/yara/yara/yara.lf.drp
md5sum: 3ef99a87a4e44513f46d42f4261f7842
- - path: output/index/yara/yara.txt.limits
+ - path: output/yara/yara/yara.txt.limits
md5sum: 4480a068db603e4c9a27bc4fa9ceaf14
- - path: output/index/yara/yara.lf.drv
+ - path: output/yara/yara/yara.lf.drv
md5sum: cf6408307fe9fd7f99c33f521bf95550
- - path: output/index/yara/yara.fasta
+ - path: output/yara/yara/yara.fasta
md5sum: 6e9fe4042a72f2345f644f239272b7e6
diff --git a/tests/subworkflows/nf-core/align_bowtie2/test.yml b/tests/subworkflows/nf-core/align_bowtie2/test.yml
index 07c0b1b4..beea38c2 100644
--- a/tests/subworkflows/nf-core/align_bowtie2/test.yml
+++ b/tests/subworkflows/nf-core/align_bowtie2/test.yml
@@ -1,9 +1,10 @@
- name: align bowtie2 single-end
command: nextflow run ./tests/subworkflows/nf-core/align_bowtie2 -entry test_align_bowtie2_single_end -c tests/config/nextflow.config
tags:
- - subworkflows/align_bowtie2
- - subworkflows/bam_sort_samtools
- - subworkflows/bam_stats_samtools
+ - subworkflows
+ # - subworkflows/align_bowtie2
+ # - subworkflows/bam_sort_samtools
+ # - subworkflows/bam_stats_samtools
# Modules
# - bowtie2
# - bowtie2/align
@@ -42,9 +43,10 @@
- name: align bowtie2 paired-end
command: nextflow run ./tests/subworkflows/nf-core/align_bowtie2 -entry test_align_bowtie2_paired_end -c tests/config/nextflow.config
tags:
- - subworkflows/align_bowtie2
- - subworkflows/bam_sort_samtools
- - subworkflows/bam_stats_samtools
+ - subworkflows
+ # - subworkflows/align_bowtie2
+ # - subworkflows/bam_sort_samtools
+ # - subworkflows/bam_stats_samtools
# Modules
# - bowtie2
# - bowtie2/align
diff --git a/tests/subworkflows/nf-core/bam_sort_samtools/test.yml b/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
index b84735e5..7dc73c80 100644
--- a/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
+++ b/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
@@ -1,15 +1,16 @@
- name: bam sort samtools single-end
command: nextflow run ./tests/subworkflows/nf-core/bam_sort_samtools -entry test_bam_sort_samtools_single_end -c tests/config/nextflow.config
tags:
- - subworkflows/bam_sort_samtools
- - subworkflows/bam_stats_samtools
+ - subworkflows
+ # - subworkflows/bam_sort_samtools
+ # - subworkflows/bam_stats_samtools
# Modules
- - samtools
- - samtools/index
- - samtools/sort
- - samtools/stats
- - samtools/idxstats
- - samtools/flagstat
+ # - samtools
+ # - samtools/index
+ # - samtools/sort
+ # - samtools/stats
+ # - samtools/idxstats
+ # - samtools/flagstat
files:
- path: ./output/samtools/test.sorted.bam
md5sum: 8b56bb7d26ced04112f712250d915aaa
@@ -25,8 +26,9 @@
- name: bam sort samtools paired-end
command: nextflow run ./tests/subworkflows/nf-core/bam_sort_samtools -entry test_bam_sort_samtools_paired_end -c tests/config/nextflow.config
tags:
- - subworkflows/bam_sort_samtools
- - subworkflows/bam_stats_samtools
+ - subworkflows
+ # - subworkflows/bam_sort_samtools
+ # - subworkflows/bam_stats_samtools
# Modules
# - samtools
# - samtools/index
diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml
index d93c95a5..2b2e45d1 100644
--- a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml
+++ b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml
@@ -1,12 +1,13 @@
- name: bam stats samtools single-end
command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c tests/config/nextflow.config
tags:
- - subworkflows/bam_stats_samtools
+ - subworkflows
+ # - subworkflows/bam_stats_samtools
# Modules
- - samtools
- - samtools/stats
- - samtools/idxstats
- - samtools/flagstat
+ # - samtools
+ # - samtools/stats
+ # - samtools/idxstats
+ # - samtools/flagstat
files:
- path: ./output/samtools/test.single_end.sorted.bam.flagstat
md5sum: 2191911d72575a2358b08b1df64ccb53
@@ -17,12 +18,13 @@
- name: bam stats samtools paired-end
command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c tests/config/nextflow.config
tags:
- - subworkflows/bam_stats_samtools
- # Modules
- - samtools
- - samtools/stats
- - samtools/idxstats
- - samtools/flagstat
+ - subworkflows
+ # - subworkflows/bam_stats_samtools
+ # # Modules
+ # - samtools
+ # - samtools/stats
+ # - samtools/idxstats
+ # - samtools/flagstat
files:
- path: ./output/samtools/test.paired_end.sorted.bam.flagstat
md5sum: 4f7ffd1e6a5e85524d443209ac97d783
diff --git a/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml b/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml
index e6d80409..63cf64f8 100644
--- a/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml
+++ b/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml
@@ -1,8 +1,9 @@
- name: gatk_create_som_pon
command: nextflow run ./tests/subworkflows/nf-core/gatk_create_som_pon -entry test_gatk_create_som_pon -c tests/config/nextflow.config
tags:
- - subworkflows/gatk_create_som_pon
- - gatk4
+ - subworkflows
+ # - subworkflows/gatk_create_som_pon
+ # - gatk4
# Modules
# - gatk4/genomicsdbimport
# - gatk4/createsomaticpanelofnormals
diff --git a/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml b/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml
index 3c6753fb..4b335065 100644
--- a/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml
+++ b/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml
@@ -1,7 +1,8 @@
- name: gatk_tumor_normal_somatic_variant_calling
command: nextflow run ./tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling -entry test_gatk_tumor_normal_somatic_variant_calling -c tests/config/nextflow.config
tags:
- - subworkflows/gatk_tumor_normal_somatic_variant_calling
+ - subworkflows
+ # - subworkflows/gatk_tumor_normal_somatic_variant_calling
# Modules
# - gatk4/mutect2
# - gatk4/learnreadorientationmodel
diff --git a/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml b/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml
index 797ae936..9d2d5c10 100644
--- a/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml
+++ b/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml
@@ -1,7 +1,8 @@
- name: gatk_tumor_only_somatic_variant_calling
command: nextflow run ./tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling -entry test_gatk_tumor_only_somatic_variant_calling -c tests/config/nextflow.config
tags:
- - subworkflows/gatk_tumor_only_somatic_variant_calling
+ - subworkflows
+ # - subworkflows/gatk_tumor_only_somatic_variant_calling
# Modules
# - gatk4/mutect2
# - gatk4/getpileupsummaries
diff --git a/tests/subworkflows/nf-core/sra_fastq/test.yml b/tests/subworkflows/nf-core/sra_fastq/test.yml
index 6f953ccf..4b75431f 100644
--- a/tests/subworkflows/nf-core/sra_fastq/test.yml
+++ b/tests/subworkflows/nf-core/sra_fastq/test.yml
@@ -1,11 +1,12 @@
- name: sra fastq single-end
command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_single_end -c tests/config/nextflow.config
tags:
- - subworkflows/sra_fastq
+ - subworkflows
+ # - subworkflows/sra_fastq
# Modules
- - sratools
- - sratools/prefetch
- - sratools/fasterqdump
+ # - sratools
+ # - sratools/prefetch
+ # - sratools/fasterqdump
files:
- path: output/sratools/SRR13255544.fastq.gz
md5sum: 1054c7b71884acdb5eed8a378f18be82
@@ -13,11 +14,12 @@
- name: sra fastq paired-end
command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_paired_end -c tests/config/nextflow.config
tags:
- - subworkflows/sra_fastq
+ - subworkflows
+ # - subworkflows/sra_fastq
# Modules
- - sratools
- - sratools/prefetch
- - sratools/fasterqdump
+ # - sratools
+ # - sratools/prefetch
+ # - sratools/fasterqdump
files:
- path: output/sratools/SRR11140744_1.fastq.gz
md5sum: 193809c784a4ea132ab2a253fa4f55b6