Merge branch 'nf-core:master' into master

.nf-core.yml

@@ -0,0 +1,10 @@
+bump-versions:
+  rseqc/junctionannotation: False
+  rseqc/bamstat: False
+  rseqc/readduplication: False
+  rseqc/readdistribution: False
+  rseqc/junctionsaturation: False
+  rseqc/inferexperiment: False
+  rseqc/innerdistance: False
+  sortmerna: False
+  malt/build: False

README.md

@@ -381,6 +381,8 @@ Please follow the steps below to run the tests locally:
 
     - See [docs on running pytest-workflow](https://pytest-workflow.readthedocs.io/en/stable/#running-pytest-workflow) for more info.
 
+> :warning: if you have a module named `build` this can conflict with some pytest internal behaviour. This results in no tests being run (i.e. recieving a message of `collected 0 items`). In this case rename the `tests/<module>/build` directry to `tests/<module>/build_test`, and update the corresponding `test.yml` accordingly. An example can be seen with the [`bowtie2/build` module tests](https://github.com/nf-core/modules/tree/master/tests/modules/bowtie2/build_test).
+
 ### Uploading to `nf-core/modules`
 
 [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`modules/`](modules) directory. Please try and keep PRs as atomic as possible to aid the reviewing process - ideally, one module addition/update per PR.
@@ -429,6 +431,16 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
 
 - All function names MUST follow the `camelCase` convention.
 
+#### Input/output options
+
+- Input channel declarations MUST be defined for all _possible_ input files (i.e. both required and optional files).
+    - Directly associated auxiliary files to an input file MAY be defined within the same input channel alongside the main input channel  (e.g. [BAM and BAI](https://github.com/nf-core/modules/blob/e937c7950af70930d1f34bb961403d9d2aa81c7d/modules/samtools/flagstat/main.nf#L22)).
+    - Other generic auxiliary files used across different input files (e.g. common reference sequences) MAY be defined using a dedicated input channel (e.g. [reference files](https://github.com/nf-core/modules/blob/3cabc95d0ed8a5a4e07b8f9b1d1f7ff9a70f61e1/modules/bwa/mem/main.nf#L21-L23)).
+
+- Named file extensions MUST be emitted for ALL output channels e.g. `path "*.txt", emit: txt`.
+
+- Optional inputs are not currently supported by Nextflow. However, passing an empty list (`[]`) instead of a file as a module parameter can be used to work around this issue.
+
 #### Module parameters
 
 - A module file SHOULD only define input and output files as command-line parameters to be executed within the process.
@@ -439,18 +451,16 @@ using a combination of `bwa` and `samtools` to output a BAM file instead of a SA
 
 - Any parameters that need to be evaluated in the context of a particular sample e.g. single-end/paired-end data MUST also be defined within the process.
 
-#### Input/output options
-
-- Named file extensions MUST be emitted for ALL output channels e.g. `path "*.txt", emit: txt`.
-
-- Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
-
 #### Resource requirements
 
 - An appropriate resource `label` MUST be provided for the module as listed in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config#L29-L46) e.g. `process_low`, `process_medium` or `process_high`.
 
 - If the tool supports multi-threading then you MUST provide the appropriate parameter using the Nextflow `task` variable e.g. `--threads $task.cpus`.
 
+- If a module contains _multiple_ tools that supports multi-threading (e.g. [piping output into a samtools command](https://github.com/nf-core/modules/blob/28b023e6f4d0d2745406d9dc6e38006882804e67/modules/bowtie2/align/main.nf#L32-L46)), you MUST assign cpus per tool such that the total number of used CPUs does not exceed `task.cpus`.
+    - For example, combining two (or more) tools that both (all) have multi-threading, this can be assigned to the variable [`split_cpus`](https://github.com/nf-core/modules/blob/28b023e6f4d0d2745406d9dc6e38006882804e67/modules/bowtie2/align/main.nf#L32)
+    - If one tool is multi-threaded and another uses a single thread, you can specify directly in the command itself e.g. with [`${task.cpus - 1}`](https://github.com/nf-core/modules/blob/6e68c1af9a514bb056c0513ebba6764efd6750fc/modules/bwa/sampe/main.nf#L42-L43)
+
 #### Software requirements
 
 [BioContainers](https://biocontainers.pro/#/) is a registry of Docker and Singularity containers automatically created from all of the software packages on [Bioconda](https://bioconda.github.io/). Where possible we will use BioContainers to fetch pre-built software containers and Bioconda to install software using Conda.

modules/allelecounter/main.nf

@@ -11,11 +11,11 @@ process ALLELECOUNTER {
         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::cancerit-allelecount=4.2.1" : null)
+    conda (params.enable_conda ? 'bioconda::cancerit-allelecount=4.3.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.2.1--h3ecb661_0"
+        container "https://depot.galaxyproject.org/singularity/cancerit-allelecount:4.3.0--h41abebc_0"
     } else {
-        container "quay.io/biocontainers/cancerit-allelecount:4.2.1--h3ecb661_0"
+        container "quay.io/biocontainers/cancerit-allelecount:4.3.0--h41abebc_0"
     }
 
     input:

modules/arriba/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/arriba/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ARRIBA {
+    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::arriba=2.1.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1"
+    } else {
+        container "quay.io/biocontainers/arriba:2.1.0--h3198e80_1"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    path fasta
+    path gtf
+
+    output:
+    tuple val(meta), path("*.fusions.tsv")          , emit: fusions
+    tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
+    path "*.version.txt"                            , emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def blacklist = (options.args.contains('-b')) ? '' : '-f blacklist'
+    """
+    arriba \\
+        -x $bam \\
+        -a $fasta \\
+        -g $gtf \\
+        -o ${prefix}.fusions.tsv \\
+        -O ${prefix}.fusions.discarded.tsv \\
+        $blacklist \\
+        $options.args
+
+    echo \$(arriba -h | grep 'Version:' 2>&1) |  sed 's/Version:\s//' > ${software}.version.txt
+    """
+}

modules/arriba/meta.yml

@@ -0,0 +1,54 @@
+name: arriba
+description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
+keywords:
+  - fusion
+  - arriba
+tools:
+  - arriba:
+      description: Fast and accurate gene fusion detection from RNA-Seq data
+      homepage: https://github.com/suhrig/arriba
+      documentation: https://arriba.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/suhrig/arriba
+      doi: "10.1101/gr.257246.119"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - fasta:
+      type: file
+      description: Assembly FASTA file
+      pattern: "*.{fasta}"
+  - gtf:
+      type: file
+      description: Annotation GTF file
+      pattern: "*.{gtf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - fusions:
+      type: file
+      description: File contains fusions which pass all of Arriba's filters.
+      pattern: "*.{fusions.tsv}"
+  - fusions_fail:
+      type: file
+      description: File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.
+      pattern: "*.{fusions.discarded.tsv}"
+
+authors:
+  - "@praveenraj2018"

modules/bcftools/concat/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bcftools/concat/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BCFTOOLS_CONCAT {
+    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::bcftools=1.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+    } else {
+        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+    }
+
+    input:
+    tuple val(meta), path(vcfs)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    path  "*.version.txt"        , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bcftools concat \\
+        --output ${prefix}.vcf.gz \\
+        $options.args \\
+        --threads $task.cpus \\
+        ${vcfs}
+
+    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    """
+}

modules/bcftools/concat/meta.yml

@@ -0,0 +1,42 @@
+name: bcftools_concat
+description: Concatenate VCF files
+keywords:
+    - variant calling
+    - concat
+    - bcftools
+    - VCF
+
+tools:
+    - concat:
+        description: |
+          Concatenate VCF files.
+        homepage: http://samtools.github.io/bcftools/bcftools.html
+        documentation: http://www.htslib.org/doc/bcftools.html
+        doi: 10.1093/bioinformatics/btp352
+input:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcfs:
+        type: files
+        description: |
+          List containing 2 or more vcf files
+          e.g. [ 'file1.vcf', 'file2.vcf' ]
+output:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF concatenated output file
+        pattern: "*.{vcf.gz}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+  - "@abhi18av"

modules/bcftools/consensus/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_CONSENSUS {
         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::bcftools=1.11' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0'
+        container 'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0'
     } else {
-        container 'quay.io/biocontainers/bcftools:1.11--h7c999a4_0'
+        container 'quay.io/biocontainers/bcftools:1.13--h3a49de5_0'
     }
 
     input:

modules/bcftools/filter/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_FILTER {
         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::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/isec/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_ISEC {
         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::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/merge/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_MERGE {
         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::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/mpileup/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_MPILEUP {
         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::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/bcftools/norm/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bcftools/norm/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BCFTOOLS_NORM {
+    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::bcftools=1.13" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+    } else {
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf)
+    path(fasta)
+
+    output:
+    tuple val(meta), path("*.gz") , emit: vcf
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bcftools norm \\
+        --fasta-ref ${fasta} \\
+        --output ${prefix}.vcf.gz \\
+        $options.args \\
+        --threads $task.cpus \\
+        ${vcf}
+
+    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    """
+}

modules/bcftools/norm/meta.yml

@@ -0,0 +1,45 @@
+name: bcftools_norm
+description: Normalize VCF file
+keywords:
+  - normalize
+  - norm
+  - variant calling
+  - VCF
+tools:
+    - norm:
+        description: |
+          Normalize VCF files.
+        homepage: http://samtools.github.io/bcftools/bcftools.html
+        documentation: http://www.htslib.org/doc/bcftools.html
+        doi: 10.1093/bioinformatics/btp352
+input:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: |
+          The vcf file to be normalized
+          e.g. 'file1.vcf'
+    - fasta:
+        type: file
+        description: FASTA reference file
+        pattern: "*.{fasta,fa}"
+output:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF normalized output file
+        pattern: "*.{vcf.gz}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@abhi18av"

modules/bcftools/reheader/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bcftools/reheader/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BCFTOOLS_REHEADER {
+    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::bcftools=1.13" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
+    } else {
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf)
+    path fai
+    path header
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "*.version.txt"             , emit: version
+
+    script:
+    def software         = getSoftwareName(task.process)
+    def prefix           = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def update_sequences = fai ? "-f $fai" : ""
+    def new_header       = header ? "-h $header" : ""
+    """
+    bcftools \\
+        reheader \\
+        $update_sequences \\
+        $new_header \\
+        $options.args \\
+        --threads $task.cpus \\
+        -o ${prefix}.vcf.gz \\
+        $vcf
+
+    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    """
+}

modules/bcftools/reheader/meta.yml

@@ -0,0 +1,51 @@
+name: bcftools_reheader
+description: Reheader a VCF file
+keywords:
+  - reheader
+  - vcf
+  - update header
+tools:
+  - reheader:
+      description: |
+        Modify header of VCF/BCF files, change sample names.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
+      doi: 10.1093/gigascience/giab008
+      licence: ['GPL']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF/BCF file
+      pattern: "*.{vcf.gz,vcf,bcf}"
+  - fai:
+      type: file
+      description: Fasta index to update header sequences with
+      pattern: "*.{fai}"
+  - header:
+      type: file
+      description: New header to add to the VCF
+      pattern: "*.{header.txt}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - vcf:
+      type: file
+      description: VCF with updated header
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@bjohnnyd"

modules/bcftools/stats/main.nf

@@ -11,11 +11,11 @@ process BCFTOOLS_STATS {
         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::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
     }
 
     input:

modules/blast/blastn/main.nf

@@ -11,11 +11,11 @@ process BLAST_BLASTN {
         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::blast=2.10.1' : null)
+    conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
+        container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
     } else {
-        container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
+        container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
     }
 
     input:

modules/blast/makeblastdb/main.nf

@@ -11,11 +11,11 @@ process BLAST_MAKEBLASTDB {
         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::blast=2.10.1' : null)
+    conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/blast:2.10.1--pl526he19e7b1_3'
+        container 'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0'
     } else {
-        container 'quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_3'
+        container 'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0'
     }
 
     input:

modules/bowtie2/build/main.nf

@@ -11,11 +11,11 @@ process BOWTIE2_BUILD {
         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::bowtie2=2.4.2' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
+        container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0'
     } else {
-        container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
+        container 'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0'
     }
 
     input:

modules/bwa/aln/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bwa/aln/main.nf

@@ -0,0 +1,67 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BWA_ALN {
+    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::bwa=0.7.17" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8"
+    } else {
+        container "quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    path index
+
+    output:
+    tuple val(meta), path("*.sai"), emit: sai
+    path "*.version.txt"                       , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    if (meta.single_end) {
+        """
+        INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
+        bwa aln \\
+            $options.args \\
+            -t $task.cpus \\
+            -f ${prefix}.sai \\
+            \$INDEX \\
+            ${reads}
+
+        echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+        """
+    } else {
+        """
+        INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
+        bwa aln \\
+            $options.args \\
+            -t $task.cpus \\
+            -f ${prefix}.1.sai \\
+            \$INDEX \\
+            ${reads[0]}
+
+        bwa aln \\
+            $options.args \\
+            -t $task.cpus \\
+            -f ${prefix}.2.sai \\
+            \$INDEX \\
+            ${reads[1]}
+
+        echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+        """
+    }
+}

modules/bwa/aln/meta.yml

@@ -0,0 +1,54 @@
+name: bwa_aln
+description: Find SA coordinates of the input reads for bwa short-read mapping
+keywords:
+  - bwa
+  - aln
+  - short-read
+  - align
+  - reference
+  - fasta
+  - map
+  - fastq
+tools:
+    - bwa:
+        description: |
+            BWA is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bio-bwa.sourceforge.net/
+        documentation: http://bio-bwa.sourceforge.net/
+        doi: "10.1093/bioinformatics/btp324"
+      licence: ['GPL v3']
+
+input:
+    - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: |
+            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+            respectively.
+    - index:
+        type: file
+        description: BWA genome index files
+        pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - sai:
+      type: file
+      description: Single or paired SA coordinate files
+      pattern: "*.sai"
+
+authors:
+  - "@jfy133"

modules/bwa/sampe/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bwa/sampe/main.nf

@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BWA_SAMPE {
+    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::bwa=0.7.17 bioconda::samtools=1.12" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
+    }
+
+    input:
+    tuple val(meta), path(reads), path(sai)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
+
+    """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
+    bwa sampe \\
+        $options.args \\
+        $read_group \\
+        \$INDEX \\
+        $sai \\
+        $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam
+
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}

modules/bwa/sampe/meta.yml

@@ -0,0 +1,58 @@
+name: bwa_sampe
+description: Convert paired-end bwa SA coordinate files to SAM format
+keywords:
+  - bwa
+  - aln
+  - short-read
+  - align
+  - reference
+  - fasta
+  - map
+  - sam
+  - bam
+tools:
+    - bwa:
+        description: |
+            BWA is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bio-bwa.sourceforge.net/
+        documentation: http://bio-bwa.sourceforge.net/
+        doi: "10.1093/bioinformatics/btp324"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information.
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: FASTQ files specified alongside meta in input channel.
+      pattern: "*.{fastq,fq}.gz"
+  - sai:
+      type: file
+      description: SAI file specified alongside meta and reads in input channel.
+      pattern: "*.sai"
+  - index:
+        type: directory
+        description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
+        pattern: "bwa/"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+
+authors:
+  - "@jfy133"

modules/bwa/samse/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bwa/samse/main.nf

@@ -0,0 +1,46 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BWA_SAMSE {
+    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::bwa=0.7.17 bioconda::samtools=1.12" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:66ed1b38d280722529bb8a0167b0cf02f8a0b488-0"
+    }
+
+    input:
+    tuple val(meta), path(reads), path(sai)
+    path index
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
+
+    """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+
+    bwa samse \\
+        $options.args \\
+        $read_group \\
+        \$INDEX \\
+        $sai \\
+        $reads | samtools sort -@ ${task.cpus - 1} -O bam - > ${prefix}.bam
+
+    echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
+    """
+}

modules/bwa/samse/meta.yml

@@ -0,0 +1,59 @@
+name: bwa_samse
+description: Convert bwa SA coordinate file to SAM format
+keywords:
+  - bwa
+  - aln
+  - short-read
+  - align
+  - reference
+  - fasta
+  - map
+  - sam
+  - bam
+
+tools:
+    - bwa:
+        description: |
+            BWA is a software package for mapping DNA sequences against
+            a large reference genome, such as the human genome.
+        homepage: http://bio-bwa.sourceforge.net/
+        documentation: http://bio-bwa.sourceforge.net/
+        doi: "10.1093/bioinformatics/btp324"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information.
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: FASTQ files specified alongside meta in input channel.
+      pattern: "*.{fastq,fq}.gz"
+  - sai:
+      type: file
+      description: SAI file specified alongside meta and reads in input channel.
+      pattern: "*.sai"
+  - index:
+        type: directory
+        description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX
+        pattern: "bwa/"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+
+authors:
+  - "@jfy133"

modules/cnvkit/main.nf

@@ -11,11 +11,11 @@ process CNVKIT {
         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::cnvkit=0.9.8" : null)
+    conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.8--py_0"
+        container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/cnvkit:0.9.8--py_0"
+        container "quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0"
     }
 
     input:

modules/cooler/digest/main.nf

@@ -5,7 +5,7 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process COOLER_DIGEST {
-    tag '$fasta'
+    tag "$fasta"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -32,7 +32,7 @@ process COOLER_DIGEST {
     """
     cooler digest \\
         $options.args \\
-        -o "${fasta.baseName}_${enzyme.replaceAll(/[^0-9a-zA-Z]+/, "_")}.bed" \\
+        -o "${fasta.baseName}_${enzyme.replaceAll(/[^0-9a-zA-Z]+/, '_')}.bed" \\
         $chromsizes \\
         $fasta \\
         $enzyme

modules/cutadapt/main.nf

@@ -11,11 +11,11 @@ process CUTADAPT {
         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::cutadapt=3.2' : null)
+    conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/cutadapt:3.2--py38h0213d0e_0'
+        container 'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1'
     } else {
-        container 'quay.io/biocontainers/cutadapt:3.2--py38h0213d0e_0'
+        container 'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1'
     }
 
     input:

modules/deeptools/computematrix/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_COMPUTEMATRIX {
         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::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/deeptools/plotfingerprint/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTFINGERPRINT {
         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::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/deeptools/plotheatmap/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTHEATMAP {
         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::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/deeptools/plotprofile/main.nf

@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTPROFILE {
         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::deeptools=3.5.0" : null)
+    conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
+        container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
     } else {
-        container "quay.io/biocontainers/deeptools:3.5.0--py_0"
+        container "quay.io/biocontainers/deeptools:3.5.1--py_0"
     }
 
     input:

modules/dragonflye/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/dragonflye/main.nf

@@ -0,0 +1,45 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DRAGONFLYE {
+    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::dragonflye=1.0.4" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/dragonflye:1.0.4--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/dragonflye:1.0.4--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("contigs.fa")                                        , emit: contigs
+    tuple val(meta), path("dragonflye.log")                                    , emit: log
+    tuple val(meta), path("{flye,miniasm,raven}.fasta")                        , emit: raw_contigs
+    tuple val(meta), path("{miniasm,raven}-unpolished.gfa"), optional:true     , emit: gfa
+    tuple val(meta), path("flye-info.txt"), optional:true                      , emit: txt
+    path "*.version.txt"                                                       , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def memory = task.memory.toGiga()
+    """
+    dragonflye \\
+        --reads ${reads} \\
+        $options.args \\
+        --cpus $task.cpus \\
+        --ram $memory \\
+        --outdir ./ \\
+        --force
+    echo \$(dragonflye --version 2>&1) | sed 's/^.*dragonflye //'  > ${software}.version.txt
+    """
+}

modules/dragonflye/meta.yml

@@ -0,0 +1,57 @@
+name: dragonflye
+description: Assemble bacterial isolate genomes from Nanopore reads
+keywords:
+  - bacterial
+  - assembly
+  - nanopore
+
+tools:
+  - dragonflye:
+      description: Microbial assembly pipeline for Nanopore reads
+      homepage: https://github.com/rpetit3/dragonflye
+      documentation: https://github.com/rpetit3/dragonflye/blob/main/README.md
+      licence: ['GPL v2']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+        type: file
+        description: Input Nanopore FASTQ file
+        pattern: "*.fastq.gz"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - contigs:
+      type: file
+      description: The final assembly produced by Dragonflye
+      pattern: "contigs.fa"
+  - log:
+      type: file
+      description: Full log file for bug reporting
+      pattern: "dragonflye.log"
+  - raw_contigs:
+      type: file
+      description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven)
+      pattern: "{flye,miniasm,raven}.fasta"
+  - txt:
+      type: file
+      description: Assembly information output by Flye
+      pattern: "flye-info.txt"
+  - gfa:
+      type: file
+      description: Assembly graph produced by Miniasm, or Raven
+      pattern: "{miniasm,raven}-unpolished.gfa"
+
+authors:
+  - "@rpetit3"

modules/dshbio/exportsegments/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/dshbio/exportsegments/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DSHBIO_EXPORTSEGMENTS {
+    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::dsh-bio=2.0.5" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(gfa)
+
+    output:
+    tuple val(meta), path("*.fa"), emit: fasta
+    path "*.version.txt"             , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    dsh-bio \\
+        export-segments \\
+        $options.args \\
+        -i $gfa \\
+        -o ${prefix}.fa
+
+    echo \$(dsh-bio --version 2>&1) | grep -o 'dsh-bio-tools .*' | cut -f2 -d ' ' > ${software}.version.txt
+    """
+}

modules/dshbio/exportsegments/meta.yml

@@ -0,0 +1,40 @@
+name: dshbio_exportsegments
+description: Export assembly segment sequences in GFA 1.0 format to FASTA format
+keywords:
+    - gfa
+    - assembly
+    - segment
+tools:
+    - dshbio:
+        description: |
+            Reads, features, variants, assemblies, alignments, genomic range trees, pangenome
+            graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3
+            or later.
+        homepage: https://github.com/heuermh/dishevelled-bio
+        documentation: https://github.com/heuermh/dishevelled-bio
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - gfa:
+        type: file
+        description: Assembly segments in GFA 1.0 format
+        pattern: "*.{gfa}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Assembly segment sequences in FASTA format
+        pattern: "*.{fa}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@heuermh"

modules/dshbio/filterbed/main.nf

@@ -11,11 +11,11 @@ process DSHBIO_FILTERBED {
         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::dsh-bio=2.0.4" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.4--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/dsh-bio:2.0.4--hdfd78af_0"
+        container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
     }
 
     input:

modules/dshbio/filtergff3/main.nf

@@ -11,11 +11,11 @@ process DSHBIO_FILTERGFF3 {
         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::dsh-bio=2.0.4" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.4--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/dsh-bio:2.0.4--hdfd78af_0"
+        container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
     }
 
     input:

modules/dshbio/splitbed/main.nf

@@ -11,11 +11,11 @@ process DSHBIO_SPLITBED {
         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::dsh-bio=2.0.4" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.4--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/dsh-bio:2.0.4--hdfd78af_0"
+        container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
     }
 
     input:

modules/dshbio/splitgff3/main.nf

@@ -11,11 +11,11 @@ process DSHBIO_SPLITGFF3 {
         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::dsh-bio=2.0.4" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.4--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/dsh-bio:2.0.5--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/dsh-bio:2.0.4--hdfd78af_0"
+        container "quay.io/biocontainers/dsh-bio:2.0.5--hdfd78af_0"
     }
 
     input:

modules/expansionhunter/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/expansionhunter/main.nf

@@ -0,0 +1,45 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process EXPANSIONHUNTER {
+    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::expansionhunter=4.0.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0"
+    } else {
+        container "quay.io/biocontainers/expansionhunter:4.0.2--he785bd8_0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path fasta
+    path variant_catalog
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: vcf
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female"
+    """
+    ExpansionHunter \\
+        $options.args \\
+        --reads $bam \\
+        --output-prefix $prefix \\
+        --reference $fasta \\
+        --variant-catalog $variant_catalog \\
+        --sex $gender
+
+    echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter //' > ${software}.version.txt
+    """
+}

modules/expansionhunter/meta.yml

@@ -0,0 +1,50 @@
+name: expansionhunter
+description: write your description here
+keywords:
+  - STR
+  - repeat_expansions
+tools:
+  - expansionhunter:
+      description: A tool for estimating repeat sizes
+      homepage: https://github.com/Illumina/ExpansionHunter
+      documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md
+      tool_dev_url: None
+      doi: "10.1093/bioinformatics/btz431"
+      licence: ['Apache v2.0']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM file
+      pattern: "*.{bam,cram}"
+  - fasta:
+      type: file
+      description: Reference genome
+      pattern: "*.{fa,fasta}"
+  - variant_catalog:
+      type: file
+      description: json file with repeat expansion sites to genotype
+      pattern: "*.{json}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', gender:'female' ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - vcf:
+      type: file
+      description: VCF with repeat expansions
+      pattern: "*.{vcf}"
+
+authors:
+  - "@jemten"

modules/fastp/main.nf

@@ -20,21 +20,24 @@ process FASTP {
 
     input:
     tuple val(meta), path(reads)
+    val   save_trimmed_fail
+    val   save_merged
 
     output:
-    tuple val(meta), path('*.trim.fastq.gz'), emit: reads
-    tuple val(meta), path('*.json')         , emit: json
-    tuple val(meta), path('*.html')         , emit: html
-    tuple val(meta), path('*.log')          , emit: log
-    path '*.version.txt'                    , emit: version
-    tuple val(meta), path('*.fail.fastq.gz'), optional:true, emit: reads_fail
+    tuple val(meta), path('*.trim.fastq.gz')  , emit: reads
+    tuple val(meta), path('*.json')           , emit: json
+    tuple val(meta), path('*.html')           , emit: html
+    tuple val(meta), path('*.log')            , emit: log
+    path '*.version.txt'                      , emit: version
+    tuple val(meta), path('*.fail.fastq.gz')  , optional:true, emit: reads_fail
+    tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
 
     script:
     // Added soft-links to original fastqs for consistent naming in MultiQC
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     if (meta.single_end) {
-        def fail_fastq = params.save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
+        def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         fastp \\
@@ -49,7 +52,8 @@ process FASTP {
         echo \$(fastp --version 2>&1) | sed -e "s/fastp //g" > ${software}.version.txt
         """
     } else {
-        def fail_fastq = params.save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+        def fail_fastq  = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+        def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
         """
         [ ! -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
@@ -61,6 +65,7 @@ process FASTP {
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
             $fail_fastq \\
+            $merge_fastq \\
             --thread $task.cpus \\
             --detect_adapter_for_pe \\
             $options.args \\

modules/fastp/meta.yml

@@ -30,7 +30,7 @@ output:
         e.g. [ id:'test', single_end:false ]
   - reads:
       type: file
-      description: The trimmed/modified fastq reads
+      description: The trimmed/modified/unmerged fastq reads
       pattern: "*trim.fastq.gz"
   - json:
       type: file
@@ -52,6 +52,10 @@ output:
       type: file
       description: Reads the failed the preprocessing
       pattern: "*fail.fastq.gz"
+  - reads_merged:
+      type: file
+      description: Reads that were successfully merged
+      pattern: "*.{merged.fastq.gz}"
 authors:
   - "@drpatelh"
   - "@kevinmenden"

modules/gubbins/main.nf

@@ -10,11 +10,11 @@ process GUBBINS {
         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=2.4.1" : null)
+    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:2.4.1--py38h197edbe_1"
+        container "https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0"
     } else {
-        container "quay.io/biocontainers/gubbins:2.4.1--py38h197edbe_1"
+        container "quay.io/biocontainers/gubbins:3.0.0--py39h5bf99c6_0"
     }
 
     input:

modules/hisat2/build/main.nf

@@ -14,11 +14,11 @@ process HISAT2_BUILD {
         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=2.2.0" : null)
+    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/hisat2:2.2.0--py37hfa133b6_4"
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
     } else {
-        container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+        container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
     }
 
     input:

modules/hisat2/extractsplicesites/main.nf

@@ -13,11 +13,11 @@ process HISAT2_EXTRACTSPLICESITES {
         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=2.2.0" : null)
+    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/hisat2:2.2.0--py37hfa133b6_4"
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3"
     } else {
-        container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+        container "quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3"
     }
 
     input:

modules/iqtree/main.nf

@@ -11,11 +11,11 @@ process IQTREE {
         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=2.1.2" : null)
+    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:2.1.2--h56fc30b_0"
+        container "https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0"
     } else {
-        container "quay.io/biocontainers/iqtree:2.1.2--h56fc30b_0"
+        container "quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0"
     }
 
     input:

modules/kallistobustools/count/main.nf

@@ -11,47 +11,45 @@ process KALLISTOBUSTOOLS_COUNT {
         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=0.26.0" : null)
+    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:0.26.0--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
+        container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
     }
 
     input:
-    tuple   val(meta),  path(reads)
-    path    index
-    path    t2g
-    path    t1c
-    path    t2c
-    val     use_t1c
-    val     use_t2c
-    val     workflow
-    val     technology
+    tuple val(meta), path(reads)
+    path  index
+    path  t2g
+    path  t1c
+    path  t2c
+    val   workflow
+    val   technology
 
     output:
-    tuple val(meta), path ("*_kallistobustools_count") , emit: kallistobustools_count
-    path "*.version.txt"                               , emit: version
+    tuple val(meta), path ("*.count"), emit: count
+    path "*.version.txt"             , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def cdna  = use_t1c ? "-c1 $t1c" : ''
-    def introns  = use_t2c ? "-c2 $t2c" : ''
+    def cdna     = t1c ? "-c1 $t1c" : ''
+    def introns  = t2c ? "-c2 $t2c" : ''
     """
     kb \\
-    count \\
-    -t $task.cpus \\
-    -i $index \\
-    -g $t2g \\
-    $cdna \\
-    $introns \\
-    --workflow $workflow \\
-    -x $technology \\
-    $options.args \\
-    -o ${prefix}_kallistobustools_count \\
-    ${reads[0]} \\
-    ${reads[1]}
+        count \\
+        -t $task.cpus \\
+        -i $index \\
+        -g $t2g \\
+        $cdna \\
+        $introns \\
+        --workflow $workflow \\
+        -x $technology \\
+        $options.args \\
+        -o ${prefix}.count \\
+        ${reads[0]} \\
+        ${reads[1]}
 
     echo \$(kb 2>&1) | sed 's/^kb_python //; s/Usage.*\$//' > ${software}.version.txt
     """

modules/kallistobustools/count/meta.yml

@@ -18,14 +18,11 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - fastq1:
-      type: file
-      description: Read 1 fastq file
-      pattern: "*.{fastq,fastq.gz}"
-  - fastq2:
-      type: file
-      description: Read 2 fastq file
-      pattern: "*.{fastq,fastq.gz}"
+  - reads:
+    type: file
+    description: |
+      List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+      respectively.
   - index:
       type: file
       description: kb-ref index file (.idx)
@@ -38,17 +35,11 @@ input:
       type: file
       description: kb ref's c1 spliced_t2c file
       pattern: "*.{cdna_t2c.txt}"
-  - use_t1c:
-      type: boolean
-      description: Whether to use the c1 txt file for RNA velocity and nucleus workflows
   - t2c:
       type: file
       description: kb ref's c2 unspliced_t2c file
       pattern: "*.{introns_t2c.txt}"
-  - use_t2c:
-      type: boolean
-      description: Whether to use the c2 txt file for RNA velocity  and nucleus workflows
-  - kb_workflow:
+  - workflow:
       type: value
       description: String value defining worfklow to use, can be one of "standard", "lamanno", "nucleus"
       pattern: "{standard,lamanno,nucleus,kite}"
@@ -57,17 +48,16 @@ input:
       description: String value defining the sequencing technology used.
       pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}"
 
-
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test']
-  - kallistobustools_count:
+  - count:
       type: file
       description: kb count output folder
-      pattern: "*_{kallistobustools_count}"
+      pattern: "*.{count}"
   - version:
       type: file
       description: File containing software version

modules/kallistobustools/ref/main.nf

@@ -11,11 +11,11 @@ process KALLISTOBUSTOOLS_REF {
         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=0.26.0" : null)
+    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:0.26.0--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/kb-python:0.26.3--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/kb-python:0.26.0--pyhdfd78af_0"
+        container "quay.io/biocontainers/kb-python:0.26.3--pyhdfd78af_0"
     }
 
     input:

modules/last/dotplot/main.nf

@@ -11,11 +11,11 @@ process LAST_DOTPLOT {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/lastal/main.nf

@@ -11,11 +11,11 @@ process LAST_LASTAL {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/lastdb/main.nf

@@ -11,11 +11,11 @@ process LAST_LASTDB {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/mafconvert/main.nf

@@ -11,11 +11,11 @@ process LAST_MAFCONVERT {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/mafswap/main.nf

@@ -11,11 +11,11 @@ process LAST_MAFSWAP {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/postmask/main.nf

@@ -11,11 +11,11 @@ process LAST_POSTMASK {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/split/main.nf

@@ -11,11 +11,11 @@ process LAST_SPLIT {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/last/train/main.nf

@@ -11,11 +11,11 @@ process LAST_TRAIN {
         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=1238" : null)
+    conda (params.enable_conda ? 'bioconda::last=1250' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/last:1238--h2e03b76_0"
+        container "https://depot.galaxyproject.org/singularity/last:1250--h2e03b76_0"
     } else {
-        container "quay.io/biocontainers/last:1238--h2e03b76_0"
+        container "quay.io/biocontainers/last:1250--h2e03b76_0"
     }
 
     input:

modules/malt/build/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/malt/build/main.nf

@@ -0,0 +1,58 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } 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:[]) }
+
+    // Do not **auto-bump** due to problem with change of version numbering between 0.4.1 and 0.5.2
+    // (originally 0.4.1 was listed as 0.41, so is always selected as 'latest' even though it is not!)
+    conda (params.enable_conda ? "bioconda::malt=0.5.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0"
+    } else {
+        container "quay.io/biocontainers/malt:0.5.2--0"
+    }
+
+    input:
+    path fastas
+    val seq_type
+    path gff
+    path map_db
+
+    output:
+    path "malt_index/"   , emit: index
+    path "*.version.txt" , emit: version
+    path "malt-build.log", emit: log
+
+    script:
+    def software = getSoftwareName(task.process)
+    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.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    def igff = gff ? "-igff ${gff}" : ""
+
+    """
+    malt-build \\
+        -J-Xmx${avail_mem}g \\
+        -v \\
+        --input ${fastas.join(' ')} \\
+        -s $seq_type \\
+        $igff \\
+        -d 'malt_index/' \\
+        -t ${task.cpus} \\
+        $options.args \\
+        -mdb ${map_db}/*.db |&tee malt-build.log
+
+    malt-build --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' | cut -d ' ' -f 2 > ${software}.version.txt
+    """
+}

modules/malt/build/meta.yml

@@ -0,0 +1,55 @@
+name: malt_build
+description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
+keywords:
+  - malt
+  - alignment
+  - metagenomics
+  - ancient DNA
+  - aDNA
+  - palaeogenomics
+  - archaeogenomics
+  - microbiome
+  - database
+tools:
+  - malt:
+      description: A tool for mapping metagenomic data
+      homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
+      documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
+      tool_dev_url: None
+      doi: "10.1038/s41559-017-0446-6"
+      licence: ['GPL v3']
+
+input:
+  - fastas:
+      type: file
+      description: Directory of, or FASTA reference files for indexing
+      pattern: "*/|*.fasta"
+  - seq_type:
+      type: string
+      description: Type of input data
+      pattern: "DNA|Protein"
+  - gff:
+      type: file
+      description: Directory of, or GFF3 files of input FASTA files
+      pattern: "*/|*.gff|*.gff3"
+  - map_db:
+      type: file
+      description: MEGAN .db file from https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html
+      pattern:
+
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - index:
+      type: directory
+      description: Directory containing MALT database index directory
+      pattern: "malt_index/"
+  - log:
+      type: file
+      description: Log file from STD out of malt-build
+      pattern: "malt-build.log"
+
+authors:
+  - "@jfy133"

modules/malt/run/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/malt/run/main.nf

@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MALT_RUN {
+
+    label 'process_high_memory'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::malt=0.5.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/malt:0.5.2--0"
+    } else {
+        container "quay.io/biocontainers/malt:0.5.2--0"
+    }
+
+    input:
+    path fastqs
+    val mode
+    path index
+
+    output:
+    path "*.rma6"                          , emit: rma6
+    path "*.{tab,text,sam}",  optional:true, emit: alignments
+    path "*.log"                           , emit: log
+    path "*.version.txt"                   , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def avail_mem = 6
+    if (!task.memory) {
+        log.info '[MALT_RUN] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
+    """
+    malt-run \\
+        -J-Xmx${avail_mem}g \\
+        -t ${task.cpus} \\
+        -v \\
+        -o . \\
+        $options.args \\
+        --inFile ${fastqs.join(' ')} \\
+        -m $mode \\
+        --index $index/ |&tee malt-run.log
+
+    echo \$(malt-run --help  2>&1) | grep -o 'version.* ' | cut -f 1 -d ',' | cut -f2 -d ' ' > ${software}.version.txt
+    """
+}

modules/malt/run/meta.yml

@@ -0,0 +1,53 @@
+name: malt_run
+description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics.
+keywords:
+  - malt
+  - alignment
+  - metagenomics
+  - ancient DNA
+  - aDNA
+  - palaeogenomics
+  - archaeogenomics
+  - microbiome
+tools:
+  - malt:
+      description: A tool for mapping metagenomic data
+      homepage: https://www.wsi.uni-tuebingen.de/lehrstuehle/algorithms-in-bioinformatics/software/malt/
+      documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf
+      tool_dev_url: None
+      doi: "10.1038/s41559-017-0446-6"
+      licence: ['GPL v3']
+
+input:
+  - fastqs:
+      type: file
+      description: Input FASTQ files
+      pattern: "*.{fastq.gz,fq.gz}"
+  - mode:
+      type: string
+      description: Program mode
+      pattern: 'Unknown|BlastN|BlastP|BlastX|Classifier'
+  - index:
+      type: directory
+      description: Index/database directory from malt-build
+      pattern: '*/'
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - rma6:
+      type: file
+      description: MEGAN6 RMA6 file
+      pattern: "*.rma6"
+  - sam:
+      type: file
+      description: Alignment files in Tab, Text or MEGAN-compatible SAM format
+      pattern: "*.{tab,txt,sam}"
+  - log:
+      type: file
+      description: Log of verbose MALT stdout
+      pattern: "malt-run.log"
+
+authors:
+  - "@jfy133"

modules/metaphlan3/main.nf

@@ -11,11 +11,11 @@ process METAPHLAN3 {
         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=3.0.10" : null)
+    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:3.0.10--pyhb7b1952_0"
+        container "https://depot.galaxyproject.org/singularity/metaphlan:3.0.12--pyhb7b1952_0"
     } else {
-        container "quay.io/biocontainers/metaphlan:3.0.10--pyhb7b1952_0"
+        container "quay.io/biocontainers/metaphlan:3.0.12--pyhb7b1952_0"
     }
 
     input:

modules/methyldackel/extract/main.nf

@@ -11,11 +11,11 @@ process METHYLDACKEL_EXTRACT {
         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=0.5.2" : null)
+    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:0.5.2--h7435645_0"
+        container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
     } else {
-        container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
+        container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
     }
 
     input:

modules/methyldackel/mbias/main.nf

@@ -11,11 +11,11 @@ process METHYLDACKEL_MBIAS {
         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=0.5.2" : null)
+    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:0.5.2--h7435645_0"
+        container "https://depot.galaxyproject.org/singularity/methyldackel:0.6.0--h22771d5_0"
     } else {
-        container "quay.io/biocontainers/methyldackel:0.5.2--h7435645_0"
+        container "quay.io/biocontainers/methyldackel:0.6.0--h22771d5_0"
     }
 
     input:

modules/minimap2/align/main.nf

@@ -11,11 +11,11 @@ process MINIMAP2_ALIGN {
         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=2.17" : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
+        container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
     } else {
-        container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
+        container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
     }
 
     input:

modules/minimap2/index/main.nf

@@ -10,11 +10,11 @@ process MINIMAP2_INDEX {
         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=2.17" : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
+        container "https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0"
     } else {
-        container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
+        container "quay.io/biocontainers/minimap2:2.21--h5bf99c6_0"
     }
 
     input:

modules/mosdepth/main.nf

@@ -11,11 +11,11 @@ process MOSDEPTH {
         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=0.3.1' : null)
+    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:0.3.1--ha7ba039_0"
+        container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0"
     } else {
-        container "quay.io/biocontainers/mosdepth:0.3.1--ha7ba039_0"
+        container "quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0"
     }
 
     input:

modules/multiqc/main.nf

@@ -10,11 +10,11 @@ process MULTIQC {
         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=1.10.1" : null)
+    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:1.10.1--py_0"
+        container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/multiqc:1.10.1--py_0"
+        container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
     }
 
     input:

modules/nanoplot/main.nf

@@ -11,11 +11,11 @@ process NANOPLOT {
         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=1.36.1" : null)
+    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:1.36.1--pyhdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0"
     } else {
-        container "quay.io/biocontainers/nanoplot:1.36.1--pyhdfd78af_0"
+        container "quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0"
     }
 
     input:

modules/nextclade/main.nf

@@ -20,35 +20,28 @@ process NEXTCLADE {
 
     input:
     tuple val(meta), path(fasta)
-    val   output_format
 
     output:
-    tuple val(meta), path("${prefix}.csv")       , optional:true, emit: csv
-    tuple val(meta), path("${prefix}.json")      , optional:true, emit: json
-    tuple val(meta), path("${prefix}.tree.json") , optional:true, emit: json_tree
-    tuple val(meta), path("${prefix}.tsv")       , optional:true, emit: tsv
+    tuple val(meta), path("${prefix}.csv")       , emit: csv
+    tuple val(meta), path("${prefix}.json")      , emit: json
+    tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
+    tuple val(meta), path("${prefix}.tsv")       , emit: tsv
     tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
     path "*.version.txt"                         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def format   = output_format
-    if (!(format in ['json', 'csv', 'tsv', 'tree', 'tsv-clades-only'])) {
-        format = 'json'
-    }
-    def extension = format
-    if (format in ['tsv-clades-only']) {
-        extension = '.clades.tsv'
-    } else if (format in ['tree']) {
-        extension = 'tree.json'
-    }
     """
     nextclade \\
         $options.args \\
         --jobs $task.cpus \\
         --input-fasta $fasta \\
-        --output-${format} ${prefix}.${extension}
+        --output-json ${prefix}.json \\
+        --output-csv ${prefix}.csv \\
+        --output-tsv ${prefix}.tsv \\
+        --output-tsv-clades-only ${prefix}.clades.tsv \\
+        --output-tree ${prefix}.tree.json
 
     echo \$(nextclade --version 2>&1) > ${software}.version.txt
     """

modules/nextclade/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: None
       tool_dev_url: https://github.com/nextstrain/nextclade
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -23,11 +23,6 @@ input:
       type: file
       description: FASTA file containing one or more consensus sequences
       pattern: "*.{fasta,fa}"
-  - output_format:
-      type: string
-      description: |
-        String for output format supported by nextclade
-        i.e one of 'json', 'csv', 'tsv', 'tree', 'tsv-clades-only'
 
 output:
   - meta:

modules/picard/collectmultiplemetrics/main.nf

@@ -11,11 +11,11 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         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=2.23.9" : null)
+    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:2.23.9--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.23.9--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/collectwgsmetrics/main.nf

@@ -11,11 +11,11 @@ process PICARD_COLLECTWGSMETRICS {
         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=2.25.0" : null)
+    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:2.25.0--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.25.0--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/filtersamreads/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/picard/filtersamreads/main.nf

@@ -0,0 +1,64 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } 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"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(readlist)
+    val filter
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard FilterSamReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    if ( filter == 'includeAligned' || filter == 'excludeAligned' ) {
+        """
+        picard \\
+            FilterSamReads \\
+            -Xmx${avail_mem}g \\
+            --INPUT $bam \\
+            --OUTPUT ${prefix}.bam \\
+            --FILTER $filter \\
+            $options.args
+
+        echo \$(picard FilterSamReads --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
+        """
+    } else if ( filter == 'includeReadList' || filter == 'excludeReadList' ) {
+        """
+        picard \\
+            FilterSamReads \\
+            -Xmx${avail_mem}g \\
+            --INPUT $bam \\
+            --OUTPUT ${prefix}.bam \\
+            --FILTER $filter \\
+            --READ_LIST_FILE $readlist \\
+            $options.args
+
+        echo \$(picard FilterSamReads --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
+        """
+    }
+}

modules/picard/filtersamreads/meta.yml

@@ -0,0 +1,51 @@
+name: picard_filtersamreads
+description: Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list
+keywords:
+  - bam
+  - filter
+tools:
+  - picard:
+      description: |
+          A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+          data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://broadinstitute.github.io/picard/
+      tool_dev_url: https://github.com/broadinstitute/picard
+      doi: ""
+      licence: ['MIT']
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam
+        pattern: "*.{bam}"
+    - filter:
+        type: value
+        description: Picard filter type
+        pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList"
+    - readlist:
+        type: file
+        description: Optional text file containing reads IDs to include or exclude
+
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Filtered BAM file
+        pattern: "*.{bam}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+  - "@jfy133"

modules/picard/markduplicates/main.nf

@@ -11,11 +11,11 @@ process PICARD_MARKDUPLICATES {
         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=2.23.9" : null)
+    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:2.23.9--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.23.9--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/mergesamfiles/main.nf

@@ -11,11 +11,11 @@ process PICARD_MERGESAMFILES {
         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=2.23.9" : null)
+    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:2.23.9--0"
+        container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/picard:2.23.9--0"
+        container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
     }
 
     input:

modules/picard/sortsam/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/picard/sortsam/main.nf

@@ -0,0 +1,49 @@
+
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } 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"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+    val sort_order
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "*.version.txt"                 , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard SortSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        SortSam \\
+        -Xmx${avail_mem}g \\
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.bam \\
+        --SORT_ORDER $sort_order
+
+    echo \$(picard SortSam --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d: > ${software}.version.txt
+    """
+}

modules/picard/sortsam/meta.yml

@@ -0,0 +1,47 @@
+name: picard_sortsam
+description: Sorts BAM/SAM files based on a variety of picard specific criteria
+keywords:
+    - sort
+    - bam
+    - sam
+tools:
+    - picard:
+        description: |
+            A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+            data and formats such as SAM/BAM/CRAM and VCF.
+        homepage: https://broadinstitute.github.io/picard/
+        documentation: https://broadinstitute.github.io/picard/
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,sam}"
+  - sort_order:
+      type: value
+      description: Picard sort order type
+      pattern: "unsorted|queryname|coordinate|duplicate|unknown"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam}"
+
+
+authors:
+  - "@jfy133"

modules/prodigal/meta.yml

@@ -1,32 +1,27 @@
 name: prodigal
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
 keywords:
   - sort
 tools:
   - prodigal:
-      ## TODO nf-core: Add a description and other details for the software below
       description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
       homepage: {}
       documentation: {}
       tool_dev_url: {}
       doi: ""
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  ## TODO nf-core: Delete / customise this example input
   - bam:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
   - meta:
       type: map
@@ -37,7 +32,6 @@ output:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"
-  ## TODO nf-core: Delete / customise this example output
   - bam:
       type: file
       description: Sorted BAM/CRAM/SAM file

modules/raxmlng/main.nf

@@ -10,11 +10,11 @@ process RAXMLNG {
         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=1.0.2" : null)
+    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:1.0.2--h7447c1b_0"
+        container "https://depot.galaxyproject.org/singularity/raxml-ng:1.0.3--h32fcf60_0"
     } else {
-        container "quay.io/biocontainers/raxml-ng:1.0.2--h7447c1b_0"
+        container "quay.io/biocontainers/raxml-ng:1.0.3--h32fcf60_0"
     }
 
     input:

modules/rseqc/bamstat/main.nf

@@ -11,7 +11,7 @@ process RSEQC_BAMSTAT {
         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" : null)
+    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 {

modules/rseqc/inferexperiment/main.nf

@@ -11,7 +11,7 @@ process RSEQC_INFEREXPERIMENT {
         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" : null)
+    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 {