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Update last module (#533)

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* Update LAST to version 1238.

* Update functions.nf to the latest devel version.

* Update test MD5sums after updating software version.

* Make portable on MacOS

* Allow input alignments to be uncompressed.

While the strategy in this family of modules is to make all inputs and
outputs compressed, this change might be useful to some users.

As of LAST 2138, `last/split` does not allow its input to be compressed.

* Search for .des file, that is guaranteed to be unique.

Some LAST indexes have more than one .bck file and it makes the name
detection crash.

In this commit, I also standardise how the names are detected.

* Use value input channel and optional output channels to handle formats.

As discussed on Slack, it is preferred to use a value input channel
instead of sneaking options through `params.args2` or `params.format`
as we did.

Likewise, optional output channels with clearly labeled format are
preferred to 'catch-all' wildcards.
This commit is contained in:
Charles Plessy 2021-06-14 20:27:27 +09:00 committed by GitHub
parent 894349b9b5
commit c8168bc351
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
22 changed files with 184 additions and 162 deletions
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13
software/last/dotplot/main.nf
View file

@ -11,23 +11,24 @@ process LAST_DOTPLOT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
tuple val(meta), path(maf) tuple val(meta), path(maf)
val(format)
output: output:
tuple val(meta), path("*.{png,gif}"), emit: plot tuple val(meta), path("*.gif"), optional:true, emit: gif
path "*.version.txt" , emit: version tuple val(meta), path("*.png"), optional:true, emit: png
path "*.version.txt" , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def format = options.args2 ? options.args2 : "png"
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
last-dotplot \\ last-dotplot \\

13
software/last/dotplot/meta.yml
View file

@ -25,12 +25,19 @@ input:
type: file type: file
description: Multiple Aligment Format (MAF) file, compressed with gzip description: Multiple Aligment Format (MAF) file, compressed with gzip
pattern: "*.{maf.gz}" pattern: "*.{maf.gz}"
- format:
type: value
description: Output format (PNG or GIF).
output: output:
- plot: - png:
type: file type: file
description: Pairwise alignment dot plot image, in PNG or other format. description: Pairwise alignment dot plot image, in PNG format.
pattern: "*.{gif,png}" pattern: "*.png"
- gif:
type: file
description: Pairwise alignment dot plot image, in GIF format.
pattern: "*.gif"
- version: - version:
type: file type: file
description: File containing software version description: File containing software version

32
software/last/lastal/functions.nf
View file

@ -1,19 +1,17 @@
/* //
* ----------------------------------------------------- // Utility functions used in nf-core DSL2 module files
* Utility functions used in nf-core DSL2 module files //
* -----------------------------------------------------
*/
/* //
* Extract name of software tool from process name using $task.process // Extract name of software tool from process name using $task.process
*/ //
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
} }
/* //
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ //
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
return options return options
} }
/* //
* Tidy up and join elements of a list to return a path string // Tidy up and join elements of a list to return a path string
*/ //
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* //
* Function to save/publish module results // Function to save/publish module results
*/ //
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)

8
software/last/lastal/main.nf
View file

@ -11,11 +11,11 @@ process LAST_LASTAL {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
@ -32,7 +32,7 @@ process LAST_LASTAL {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def trained_params = param_file ? "-p ${param_file}" : '' def trained_params = param_file ? "-p ${param_file}" : ''
""" """
INDEX_NAME=\$(basename \$(ls $index/*.bck) .bck) INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
lastal \\ lastal \\
$trained_params \\ $trained_params \\
$options.args \\ $options.args \\

6
software/last/lastdb/main.nf
View file

@ -11,11 +11,11 @@ process LAST_LASTDB {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:

22
software/last/mafconvert/main.nf
View file

@ -11,26 +11,34 @@ process LAST_MAFCONVERT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
tuple val(meta), path(maf) tuple val(meta), path(maf)
val(format)
output: output:
tuple val(meta), path("*.{axt,blast,blasttab,chain,gff,html,psl,sam,tab}.gz"), emit: alm tuple val(meta), path("*.axt.gz"), optional:true, emit: axt_gz
path "*.version.txt" , emit: version tuple val(meta), path("*.blast.gz"), optional:true, emit: blast_gz
tuple val(meta), path("*.blasttab.gz"), optional:true, emit: blasttab_gz
tuple val(meta), path("*.chain.gz"), optional:true, emit: chain_gz
tuple val(meta), path("*.gff.gz"), optional:true, emit: gff_gz
tuple val(meta), path("*.html.gz"), optional:true, emit: html_gz
tuple val(meta), path("*.psl.gz"), optional:true, emit: psl_gz
tuple val(meta), path("*.sam.gz"), optional:true, emit: sam_gz
tuple val(meta), path("*.tab.gz"), optional:true, emit: tab_gz
path "*.version.txt" , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def format = params.options.format ? params.options.format : "tab"
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
zcat $maf | maf-convert $options.args $format | gzip --no-name \\ maf-convert $options.args $format $maf | gzip --no-name \\
> ${prefix}.${format}.gz > ${prefix}.${format}.gz
# maf-convert has no --version option but lastdb (part of the same package) has. # maf-convert has no --version option but lastdb (part of the same package) has.

45
software/last/mafconvert/meta.yml
View file

@ -22,8 +22,11 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- maf: - maf:
type: file type: file
description: Multiple Aligment Format (MAF) file, compressed with gzip description: Multiple Aligment Format (MAF) file, optionally compressed with gzip
pattern: "*.{maf.gz}" pattern: "*.{maf.gz,maf}"
- format:
type: value
description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab)
output: output:
- meta: - meta:
@ -35,10 +38,42 @@ output:
type: file type: file
description: File containing software version description: File containing software version
pattern: "*.{version.txt}" pattern: "*.{version.txt}"
- alm: - axt_gz:
type: file type: file
description: Gzipped pairwise alignmnet in TAB or other formats description: Gzipped pairwise alignment in Axt (Blastz) format (optional)
pattern: "*.{axt,blast,blasttab,chain,gff,html,psl,sam,tab}.gz" pattern: "*.axt.gz"
- blast_gz:
type: file
description: Gzipped pairwise alignment in blast format (optional)
pattern: "*.blast.gz"
- blasttab_gz:
type: file
description: Gzipped pairwise alignment in blasttab format (optional)
pattern: "*.blasttab.gz"
- chain_gz:
type: file
description: Gzipped pairwise alignment in UCSC chain format (optional)
pattern: "*.chain.gz"
- gff_gz:
type: file
description: Gzipped pairwise alignment in GFF format (optional)
pattern: "*.gff.gz"
- html_gz:
type: file
description: Gzipped pairwise alignment in HTML format (optional)
pattern: "*.html.gz"
- psl_gz:
type: file
description: Gzipped pairwise alignment in PSL (BLAT) format (optional)
pattern: "*.psl.gz"
- SAM:
type: file
description: Gzipped pairwise alignment in SAM format (optional)
pattern: "*.sam.gz"
- tab:
type: file
description: Gzipped pairwise alignment in TAB format (optional)
pattern: "*.tab.gz"
authors: authors:
- "@aleksandrabliznina" - "@aleksandrabliznina"

32
software/last/mafswap/functions.nf
View file

@ -1,19 +1,17 @@
/* //
* ----------------------------------------------------- // Utility functions used in nf-core DSL2 module files
* Utility functions used in nf-core DSL2 module files //
* -----------------------------------------------------
*/
/* //
* Extract name of software tool from process name using $task.process // Extract name of software tool from process name using $task.process
*/ //
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
} }
/* //
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ //
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
return options return options
} }
/* //
* Tidy up and join elements of a list to return a path string // Tidy up and join elements of a list to return a path string
*/ //
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* //
* Function to save/publish module results // Function to save/publish module results
*/ //
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)

8
software/last/mafswap/main.nf
View file

@ -11,11 +11,11 @@ process LAST_MAFSWAP {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
@ -29,7 +29,7 @@ process LAST_MAFSWAP {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
zcat $maf | maf-swap $options.args | gzip --no-name > ${prefix}.swapped.maf.gz maf-swap $options.args $maf | gzip --no-name > ${prefix}.swapped.maf.gz
# maf-swap has no --version option but lastdb, part of the same package, has. # maf-swap has no --version option but lastdb, part of the same package, has.
echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt echo \$(lastdb --version 2>&1) | sed 's/lastdb //' > ${software}.version.txt

4
software/last/mafswap/meta.yml
View file

@ -22,8 +22,8 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- maf: - maf:
type: file type: file
description: Multiple Aligment Format (MAF) file, compressed with gzip description: Multiple Aligment Format (MAF) file, optionally compressed with gzip
pattern: "*.{maf.gz}" pattern: "*.{maf.gz,maf}"
output: output:
- maf: - maf:

32
software/last/postmask/functions.nf
View file

@ -1,19 +1,17 @@
/* //
* ----------------------------------------------------- // Utility functions used in nf-core DSL2 module files
* Utility functions used in nf-core DSL2 module files //
* -----------------------------------------------------
*/
/* //
* Extract name of software tool from process name using $task.process // Extract name of software tool from process name using $task.process
*/ //
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
} }
/* //
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ //
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
return options return options
} }
/* //
* Tidy up and join elements of a list to return a path string // Tidy up and join elements of a list to return a path string
*/ //
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* //
* Function to save/publish module results // Function to save/publish module results
*/ //
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)

8
software/last/postmask/main.nf
View file

@ -11,11 +11,11 @@ process LAST_POSTMASK {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
@ -30,7 +30,7 @@ process LAST_POSTMASK {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate" if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate"
""" """
zcat $maf | last-postmask $options.args | gzip --no-name > ${prefix}.maf.gz last-postmask $options.args $maf | gzip --no-name > ${prefix}.maf.gz
# last-postmask does not have a --version option # last-postmask does not have a --version option
echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt echo \$(lastal --version 2>&1) | sed 's/lastal //' > ${software}.version.txt

4
software/last/postmask/meta.yml
View file

@ -22,8 +22,8 @@ input:
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- maf: - maf:
type: file type: file
description: Multiple Aligment Format (MAF) file, compressed with gzip description: Multiple Aligment Format (MAF) file, optionally compressed with gzip
pattern: "*.{maf.gz}" pattern: "*.{maf.gz,maf}"
output: output:
- maf: - maf:

32
software/last/split/functions.nf
View file

@ -1,19 +1,17 @@
/* //
* ----------------------------------------------------- // Utility functions used in nf-core DSL2 module files
* Utility functions used in nf-core DSL2 module files //
* -----------------------------------------------------
*/
/* //
* Extract name of software tool from process name using $task.process // Extract name of software tool from process name using $task.process
*/ //
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
} }
/* //
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ //
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
return options return options
} }
/* //
* Tidy up and join elements of a list to return a path string // Tidy up and join elements of a list to return a path string
*/ //
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* //
* Function to save/publish module results // Function to save/publish module results
*/ //
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)

8
software/last/split/main.nf
View file

@ -11,11 +11,11 @@ process LAST_SPLIT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
@ -29,7 +29,7 @@ process LAST_SPLIT {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
zcat $maf | last-split $options.args | gzip --no-name > ${prefix}.maf.gz zcat < $maf | last-split $options.args | gzip --no-name > ${prefix}.maf.gz
echo \$(last-split --version 2>&1) | sed 's/last-split //' > ${software}.version.txt echo \$(last-split --version 2>&1) | sed 's/last-split //' > ${software}.version.txt
""" """

32
software/last/train/functions.nf
View file

@ -1,19 +1,17 @@
/* //
* ----------------------------------------------------- // Utility functions used in nf-core DSL2 module files
* Utility functions used in nf-core DSL2 module files //
* -----------------------------------------------------
*/
/* //
* Extract name of software tool from process name using $task.process // Extract name of software tool from process name using $task.process
*/ //
def getSoftwareName(task_process) { def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
} }
/* //
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/ //
def initOptions(Map args) { def initOptions(Map args) {
def Map options = [:] def Map options = [:]
options.args = args.args ?: '' options.args = args.args ?: ''
@ -26,18 +24,18 @@ def initOptions(Map args) {
return options return options
} }
/* //
* Tidy up and join elements of a list to return a path string // Tidy up and join elements of a list to return a path string
*/ //
def getPathFromList(path_list) { def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/') return paths.join('/')
} }
/* //
* Function to save/publish module results // Function to save/publish module results
*/ //
def saveFiles(Map args) { def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) { if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options) def ioptions = initOptions(args.options)

8
software/last/train/main.nf
View file

@ -11,11 +11,11 @@ process LAST_TRAIN {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } 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=1219" : null) conda (params.enable_conda ? "bioconda::last=1238" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/last:1219--h2e03b76_0" container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
} else { } else {
container "quay.io/biocontainers/last:1219--h2e03b76_0" container "quay.io/biocontainers/last:1238--h2e03b76_0"
} }
input: input:
@ -30,7 +30,7 @@ process LAST_TRAIN {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
INDEX_NAME=`find -L lastdb/ -name "*.bck" | sed 's/.bck//' | sed 's,lastdb/,,'` INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
last-train \\ last-train \\
$options.args \\ $options.args \\

12
tests/software/last/dotplot/main.nf
View file

@ -9,15 +9,5 @@ workflow test_last_dotplot {
input = [ [ id:'test' ], // meta map input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ] file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
LAST_DOTPLOT ( input ) LAST_DOTPLOT ( input, "png" )
}
include { LAST_DOTPLOT as LAST_DOTPLOT_GIF } from '../../../../software/last/dotplot/main.nf' addParams( options: [args2:'gif'] )
workflow test_last_dotplot_gif {
input = [ [ id:'test' ], // meta map
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
LAST_DOTPLOT_GIF ( input )
} }

11
tests/software/last/dotplot/test.yml
View file

@ -1,17 +1,8 @@
- name: last dotplot test_last_dotplot - name: last dotplot test_last_dotplot
command: nextflow run tests/software/last/dotplot -entry test_last_dotplot -c tests/config/nextflow.config command: nextflow run tests/software/last/dotplot -entry test_last_dotplot -c tests/config/nextflow.config
tags: tags:
- last
- last/dotplot - last/dotplot
- last
files: files:
- path: output/last/test.png - path: output/last/test.png
md5sum: 6189aaf96f522cdb664869724997bbcd md5sum: 6189aaf96f522cdb664869724997bbcd
- name: last dotplot test_last_dotplot_gif
command: nextflow run tests/software/last/dotplot -entry test_last_dotplot_gif -c tests/config/nextflow.config
tags:
- last
- last/dotplot
files:
- path: output/last/test.gif
md5sum: 1dd2c85fb5495ca0e85c4ef1dcfce220

4
tests/software/last/lastal/test.yml
View file

@ -5,7 +5,7 @@
- last/lastal - last/lastal
files: files:
- path: output/last/contigs.genome.maf.gz - path: output/last/contigs.genome.maf.gz
md5sum: 33e9098d8242b0aac829339c03fe94aa md5sum: 2fc56553282d0826310bdef16a55e587
- path: output/untar/lastdb/genome.bck - path: output/untar/lastdb/genome.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/untar/lastdb/genome.des - path: output/untar/lastdb/genome.des
@ -28,7 +28,7 @@
- last/lastal - last/lastal
files: files:
- path: output/last/contigs.genome.maf.gz - path: output/last/contigs.genome.maf.gz
md5sum: 3a0f42e76da9549748983ac4d7ff7473 md5sum: f50557bed5430b42de7b0d5d61075cf0
- path: output/untar/lastdb/genome.bck - path: output/untar/lastdb/genome.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/untar/lastdb/genome.des - path: output/untar/lastdb/genome.des

8
tests/software/last/lastdb/test.yml
View file

@ -1,15 +1,15 @@
- name: last lastdb test_last_lastdb - name: last lastdb test_last_lastdb
command: nextflow run tests/software/last/lastdb -entry test_last_lastdb -c tests/config/nextflow.config command: nextflow run tests/software/last/lastdb -entry test_last_lastdb -c tests/config/nextflow.config
tags: tags:
- last
- last/lastdb - last/lastdb
- last
files: files:
- path: output/last/lastdb/test.bck - path: output/last/lastdb/test.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/last/lastdb/test.des - path: output/last/lastdb/test.des
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
- path: output/last/lastdb/test.prj - path: output/last/lastdb/test.prj
md5sum: 489715f14b0fea6273822696e72357f9 md5sum: 2c981eb9b9d2012d8413946a5b378f20
- path: output/last/lastdb/test.sds - path: output/last/lastdb/test.sds
md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2 md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
- path: output/last/lastdb/test.ssp - path: output/last/lastdb/test.ssp
@ -22,15 +22,15 @@
- name: last lastdb test_last_lastdb_gzipped_input - name: last lastdb test_last_lastdb_gzipped_input
command: nextflow run tests/software/last/lastdb -entry test_last_lastdb_gzipped_input -c tests/config/nextflow.config command: nextflow run tests/software/last/lastdb -entry test_last_lastdb_gzipped_input -c tests/config/nextflow.config
tags: tags:
- last
- last/lastdb - last/lastdb
- last
files: files:
- path: output/last/lastdb/test.bck - path: output/last/lastdb/test.bck
md5sum: 8692b1229b1fff1c2d39c4c610ff842b md5sum: 8692b1229b1fff1c2d39c4c610ff842b
- path: output/last/lastdb/test.des - path: output/last/lastdb/test.des
md5sum: 26ab49015cc572172b9efa50fc5190bc md5sum: 26ab49015cc572172b9efa50fc5190bc
- path: output/last/lastdb/test.prj - path: output/last/lastdb/test.prj
md5sum: a302beb8b8b884d8450055ede61e973b md5sum: aec51a18da1c2361aaca70dd16eb7b7b
- path: output/last/lastdb/test.sds - path: output/last/lastdb/test.sds
md5sum: cad9927d4bd161257e98165ad755d8e4 md5sum: cad9927d4bd161257e98165ad755d8e4
- path: output/last/lastdb/test.ssp - path: output/last/lastdb/test.ssp

4
tests/software/last/mafconvert/main.nf
View file

@ -2,12 +2,12 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { LAST_MAFCONVERT } from '../../../../software/last/mafconvert/main.nf' addParams( options: ['format':'psl'] ) include { LAST_MAFCONVERT } from '../../../../software/last/mafconvert/main.nf' addParams( options: [:] )
workflow test_last_mafconvert { workflow test_last_mafconvert {
input = [ [ id:'contigs.genome' ], // meta map input = [ [ id:'contigs.genome' ], // meta map
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ] file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) ]
LAST_MAFCONVERT ( input ) LAST_MAFCONVERT ( input, "psl" )
} }