Merge branch 'master' into bat-test

.gitpod.yml

@@ -1,10 +1,14 @@
-# List the start up tasks. Learn more https://www.gitpod.io/docs/config-start-tasks/
-tasks:
-  - name: Install Nextflow
-    init: |
-      curl -s https://get.nextflow.io | bash
-      sudo mv nextflow /usr/local/bin
+image: nfcore/gitpod:latest
 
-  - name: Install pytest-workflow
-    init: |
-      pip install pytest-workflow
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore                 # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow                 # Highlight indentation level
+    - streetsidesoftware.code-spell-checker  # Spelling checker for source code

.nf-core.yml

@@ -1,3 +1,4 @@
+repository_type: modules
 bump-versions:
   rseqc/junctionannotation: False
   rseqc/bamstat: False

modules/abacas/main.nf

@@ -15,6 +15,9 @@ process ABACAS {
     tuple val(meta), path('*.abacas*'), emit: results
     path "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/adapterremoval/main.nf

@@ -15,6 +15,9 @@ process ADAPTERREMOVAL {
     tuple val(meta), path('*.log')     , emit: log
     path "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/agrvate/main.nf

@@ -15,6 +15,9 @@ process AGRVATE {
     path "${fasta.baseName}-results"                                                , emit: results_dir
     path "versions.yml"                                                             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/allelecounter/main.nf

@@ -16,6 +16,9 @@ process ALLELECOUNTER {
     tuple val(meta), path("*.alleleCount"), emit: allelecount
     path "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/amps/main.nf

@@ -18,6 +18,9 @@ process AMPS {
     path "results/pdf_candidate_profiles/"     , emit: candidate_pdfs
     path "versions.yml"                        , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/arriba/main.nf

@@ -17,6 +17,9 @@ process ARRIBA {
     tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
     path "versions.yml"                             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/artic/guppyplex/main.nf

@@ -14,6 +14,9 @@ process ARTIC_GUPPYPLEX {
     tuple val(meta), path("*.fastq.gz"), emit: fastq
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/artic/minion/main.nf

@@ -31,6 +31,9 @@ process ARTIC_MINION {
     tuple val(meta), path("*.json"), optional:true                    , emit: json
     path  "versions.yml"                                              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/assemblyscan/main.nf

@@ -14,6 +14,9 @@ process ASSEMBLYSCAN {
     tuple val(meta), path("*.json"), emit: json
     path "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/ataqv/ataqv/main.nf

@@ -19,6 +19,9 @@ process ATAQV_ATAQV {
     tuple val(meta), path("*.problems")  , emit: problems, optional: true
     path "versions.yml"                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bakta/main.nf

@@ -25,6 +25,9 @@ process BAKTA {
     tuple val(meta), path("${prefix}.tsv")              , emit: tsv
     path "versions.yml"                                 , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/bamaligncleaner/main.nf

@@ -14,6 +14,9 @@ process BAMALIGNCLEANER {
     tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bamcmp/main.nf

@@ -0,0 +1,38 @@
+def VERSION = '2.2'
+process BAMCMP {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
+        'quay.io/biocontainers/bamcmp:2.2--h05f6578_0' }"
+
+    input:
+    tuple val(meta), path(sample), path(contaminant)
+
+    output:
+    tuple val(meta), path("*primary.bam")      , emit: bam
+    tuple val(meta), path("*contamination.bam"), emit: contamination_bam
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bamcmp \\
+        -1 $sample \\
+        -2 $contaminant \\
+        -A ${prefix}_primary.bam \\
+        -B ${prefix}_contamination.bam \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamcmp: $VERSION
+    END_VERSIONS
+    """
+
+}

modules/bamcmp/meta.yml

@@ -0,0 +1,57 @@
+name: bamcmp
+description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
+keywords:
+  - filter
+  - xenograft
+  - host
+  - graft
+  - contamination
+  - mouse
+
+tools:
+  - bamcmp:
+      description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
+                    sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
+                    reads which multimap to the contamination genome will be spuriously kept.
+      homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
+      documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
+      tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
+      doi: "10.1158/1541-7786.MCR-16-0431"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+
+  - sample:
+      type: file
+      description: BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)
+      pattern: "*.{bam,cram,sam}"
+
+  - contaminant:
+      type: file
+      description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - bam:
+      type: file
+      description: Bam file containing the reads which align better to the primary genome.
+      pattern: "*.{bam,cram,sam}"
+
+  - bam:
+      type: file
+      description: Bam file containing the reads which align better to the contaminant genome.
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@kmurat1"
+  - "@sppearce"

modules/bamtools/convert/main.nf

@@ -0,0 +1,41 @@
+process BAMTOOLS_CONVERT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
+        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
+    path "versions.yml"                                              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
+    if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
+    m = args =~ /-format ([a-z]+)/
+    ext = m[0][1]
+
+
+    """
+    bamtools \\
+        convert \\
+        $args \\
+        -in $bam \\
+        -out ${prefix}.${ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
+    END_VERSIONS
+    """
+}

modules/bamtools/convert/meta.yml

@@ -0,0 +1,52 @@
+name: bamtools_convert
+description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
+keywords:
+  - bamtools
+  - bamtools/convert
+  - bam
+  - convert
+  - bed
+  - fasta
+  - fastq
+  - json
+  - pileup
+  - sam
+  - yaml
+tools:
+  - bamtools:
+      description: C++ API & command-line toolkit for working with BAM data
+      homepage: http://github.com/pezmaster31/bamtools
+      documentation: https://github.com/pezmaster31/bamtools/wiki
+      tool_dev_url: http://github.com/pezmaster31/bamtools
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  ## TODO nf-core: Delete / customise this example output
+  - out:
+      type: file
+      description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
+      pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
+
+authors:
+  - "@sguizard"

modules/bamtools/split/main.nf

@@ -14,6 +14,9 @@ process BAMTOOLS_SPLIT {
     tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bamutil/trimbam/main.nf

@@ -14,6 +14,9 @@ process BAMUTIL_TRIMBAM {
     tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bandage/image/main.nf

@@ -15,6 +15,9 @@ process BANDAGE_IMAGE {
     tuple val(meta), path('*.svg'), emit: svg
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bbmap/align/main.nf

@@ -16,6 +16,9 @@ process BBMAP_ALIGN {
     tuple val(meta), path("*.log"), emit: log
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bbmap/bbduk/main.nf

@@ -16,6 +16,9 @@ process BBMAP_BBDUK {
     tuple val(meta), path('*.log')     , emit: log
     path "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bbmap/bbsplit/main.nf

@@ -20,6 +20,9 @@ process BBMAP_BBSPLIT {
     tuple val(meta), path('*txt')             , optional:true, emit: stats
     path "versions.yml"                       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bbmap/index/main.nf

@@ -14,6 +14,9 @@ process BBMAP_INDEX {
     path 'ref'                    , emit: index
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bcftools/concat/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_CONCAT {
     tuple val(meta), path("*.gz"), emit: vcf
     path  "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/bcftools/consensus/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_CONSENSUS {
     tuple val(meta), path('*.fa'), emit: fasta
     path  "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/filter/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_FILTER {
     tuple val(meta), path("*.gz"), emit: vcf
     path  "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/index/main.nf

@@ -15,6 +15,9 @@ process BCFTOOLS_INDEX {
     tuple val(meta), path("*.tbi"), optional:true, emit: tbi
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/isec/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_ISEC {
     tuple val(meta), path("${prefix}"), emit: results
     path  "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/bcftools/merge/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_MERGE {
     tuple val(meta), path("*.gz"), emit: vcf
     path  "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/bcftools/mpileup/main.nf

@@ -19,6 +19,9 @@ process BCFTOOLS_MPILEUP {
     tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/bcftools/norm/main.nf

@@ -15,6 +15,9 @@ process BCFTOOLS_NORM {
     tuple val(meta), path("*.gz") , emit: vcf
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/query/main.nf

@@ -8,30 +8,32 @@ process BCFTOOLS_QUERY {
         'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(index)
-    path(regions)
-    path(targets)
-    path(samples)
+    tuple val(meta), path(vcf), path(tbi)
+    path regions
+    path targets
+    path samples
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
+    tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def regions_file = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
-
     """
     bcftools query \\
-        --output ${prefix}.vcf.gz \\
-        ${regions_file} \\
-        ${targets_file} \\
-        ${samples_file} \\
+        --output ${prefix}.txt \\
+        $regions_file \\
+        $targets_file \\
+        $samples_file \\
         $args \\
-        ${vcf}
+        $vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/bcftools/query/meta.yml

@@ -23,22 +23,20 @@ input:
         type: file
         description: |
           The vcf file to be qeuried.
-          e.g. 'file.vcf'
-    - index:
+        pattern: "*.{vcf.gz, vcf}"
+    - tbi:
         type: file
         description: |
           The tab index for the VCF file to be inspected.
-          e.g. 'file.tbi'
+        pattern: "*.tbi"
     - regions:
         type: file
         description: |
           Optionally, restrict the operation to regions listed in this file.
-          e.g. 'file.vcf'
     - targets:
         type: file
         description: |
           Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
-          e.g. 'file.vcf'
     - samples:
         type: file
         description: |
@@ -50,13 +48,14 @@ output:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - vcf:
+    - txt:
         type: file
-        description: VCF query output file
-        pattern: "*.{vcf.gz}"
+        description: BCFTools query output file
+        pattern: "*.txt"
     - versions:
         type: file
         description: File containing software versions
         pattern: "versions.yml"
 authors:
   - "@abhi18av"
+  - "@drpatelh"

modules/bcftools/reheader/main.nf

@@ -16,6 +16,9 @@ process BCFTOOLS_REHEADER {
     tuple val(meta), path("*.vcf.gz"), emit: vcf
     path "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/sort/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_SORT {
     tuple val(meta), path("*.gz"), emit: vcf
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/stats/main.nf

@@ -14,6 +14,9 @@ process BCFTOOLS_STATS {
     tuple val(meta), path("*stats.txt"), emit: stats
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bcftools/view/main.nf

@@ -17,6 +17,9 @@ process BCFTOOLS_VIEW {
     tuple val(meta), path("*.gz") , emit: vcf
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/bamtobed/main.nf

@@ -14,6 +14,9 @@ process BEDTOOLS_BAMTOBED {
     tuple val(meta), path("*.bed"), emit: bed
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/complement/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_COMPLEMENT {
     tuple val(meta), path('*.bed'), emit: bed
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/genomecov/main.nf

@@ -16,6 +16,9 @@ process BEDTOOLS_GENOMECOV {
     tuple val(meta), path("*.${extension}"), emit: genomecov
     path  "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args_list = args.tokenize()

modules/bedtools/getfasta/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_GETFASTA {
     path "*.fa"         , emit: fasta
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${bed.baseName}"

modules/bedtools/intersect/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_INTERSECT {
     tuple val(meta), path("*.${extension}"), emit: intersect
     path  "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/makewindows/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_MAKEWINDOWS {
     tuple val(meta), path("*.tab"), emit: tab
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/maskfasta/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_MASKFASTA {
     tuple val(meta), path("*.fa"), emit: fasta
     path "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/merge/main.nf

@@ -14,6 +14,9 @@ process BEDTOOLS_MERGE {
     tuple val(meta), path('*.bed'), emit: bed
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/slop/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_SLOP {
     tuple val(meta), path("*.bed"), emit: bed
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/sort/main.nf

@@ -15,6 +15,9 @@ process BEDTOOLS_SORT {
     tuple val(meta), path("*.${extension}"), emit: sorted
     path  "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bedtools/subtract/main.nf

@@ -14,6 +14,9 @@ process BEDTOOLS_SUBTRACT {
     tuple val(meta), path("*.bed"), emit: bed
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bismark/align/main.nf

@@ -17,6 +17,9 @@ process BISMARK_ALIGN {
     tuple val(meta), path("*fq.gz")     , optional:true, emit: unmapped
     path "versions.yml"                 , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bismark/deduplicate/main.nf

@@ -15,6 +15,9 @@ process BISMARK_DEDUPLICATE {
     tuple val(meta), path("*.deduplication_report.txt"), emit: report
     path  "versions.yml"                               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bismark/genomepreparation/main.nf

@@ -14,6 +14,9 @@ process BISMARK_GENOMEPREPARATION {
     path "BismarkIndex" , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bismark/methylationextractor/main.nf

@@ -19,6 +19,9 @@ process BISMARK_METHYLATIONEXTRACTOR {
     tuple val(meta), path("*.M-bias.txt")          , emit: mbias
     path "versions.yml"                            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def seqtype  = meta.single_end ? '-s' : '-p'

modules/bismark/report/main.nf

@@ -14,6 +14,9 @@ process BISMARK_REPORT {
     tuple val(meta), path("*report.{html,txt}"), emit: report
     path  "versions.yml"                       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bismark/summary/main.nf

@@ -17,6 +17,9 @@ process BISMARK_SUMMARY {
     path  "*report.{html,txt}", emit: summary
     path  "versions.yml"      , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/blast/blastn/main.nf

@@ -15,6 +15,9 @@ process BLAST_BLASTN {
     tuple val(meta), path('*.blastn.txt'), emit: txt
     path "versions.yml"                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/blast/makeblastdb/main.nf

@@ -14,6 +14,9 @@ process BLAST_MAKEBLASTDB {
     path 'blast_db'     , emit: db
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bowtie/align/main.nf

@@ -17,6 +17,9 @@ process BOWTIE_ALIGN {
     path  "versions.yml"          , emit: versions
     tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/bowtie/build/main.nf

@@ -14,6 +14,9 @@ process BOWTIE_BUILD {
     path 'bowtie'       , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bowtie2/align/main.nf

@@ -18,6 +18,9 @@ process BOWTIE2_ALIGN {
     tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
     path  "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/bowtie2/build/main.nf

@@ -14,6 +14,9 @@ process BOWTIE2_BUILD {
     path 'bowtie2'      , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bwa/aln/main.nf

@@ -15,6 +15,9 @@ process BWA_ALN {
     tuple val(meta), path("*.sai"), emit: sai
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bwa/index/main.nf

@@ -14,6 +14,9 @@ process BWA_INDEX {
     path "bwa"         , emit: index
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bwa/mem/main.nf

@@ -16,6 +16,9 @@ process BWA_MEM {
     tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/bwa/sampe/main.nf

@@ -15,6 +15,9 @@ process BWA_SAMPE {
     tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bwa/samse/main.nf

@@ -15,6 +15,9 @@ process BWA_SAMSE {
     tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/bwamem2/index/main.nf

@@ -14,6 +14,9 @@ process BWAMEM2_INDEX {
     path "bwamem2"      , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/bwamem2/mem/main.nf

@@ -16,6 +16,9 @@ process BWAMEM2_MEM {
     tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/bwameth/align/main.nf

@@ -15,6 +15,9 @@ process BWAMETH_ALIGN {
     tuple val(meta), path("*.bam"), emit: bam
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/bwameth/index/main.nf

@@ -14,6 +14,9 @@ process BWAMETH_INDEX {
     path "bwameth"      , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/cat/cat/main.nf

@@ -14,6 +14,9 @@ process CAT_CAT {
     path "${file_out}*" , emit: file_out
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/cat/fastq/main.nf

@@ -14,6 +14,9 @@ process CAT_FASTQ {
     tuple val(meta), path("*.merged.fastq.gz"), emit: reads
     path "versions.yml"                       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/cellranger/.gitignore

@@ -1 +1,2 @@
 cellranger-*.tar.gz
+bcl2fastq2-*.zip

modules/cellranger/Dockerfile

@@ -1,15 +1,22 @@
+# Dockerfile to create container with Cell Ranger v6.1.2
+# Push to nfcore/cellranger:<VER>
+
 FROM continuumio/miniconda3:4.8.2
 LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \
     description="Docker image containing Cell Ranger"
-# Disclaimer: this container is not provided nor supported by 10x Genomics.
+# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
 
 # Install procps and clean apt cache
 RUN apt-get update --allow-releaseinfo-change \
-    && apt-get install -y procps \
+    && apt-get install -y \
+    cpio \
+    procps \
+    rpm2cpio \
+    unzip \
     && apt-get clean -y && rm -rf /var/lib/apt/lists/*
 
 # Copy pre-downloaded cellranger file
-ENV CELLRANGER_VER 6.0.2
+ENV CELLRANGER_VER=6.1.2
 COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
 
 # Install cellranger

modules/cellranger/README.md

@@ -1,18 +1,24 @@
 # Updating the docker container and making a new module release
 
-Cell Ranger is a commercial tool by 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger version in the container and pushing the update to Dockerhub needs to be done manually.
+Cell Ranger is a commercial tool from 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
 
-1. Navigate to the [Cell Ranger download page](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) and download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
+1. Navigate to the appropriate download page.
+        - [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
 
-2. Edit the Dockerfile: update the Cell Ranger version in this line:
+2. Edit the Dockerfile. Update the Cell Ranger versions in this line:
 
     ```bash
-    ENV CELLRANGER_VER <VERSION>
+    ENV CELLRANGER_VER=<VERSION>
     ```
 
-3. Create the container:
+3. Create and test the container:
 
     ```bash
     docker build . -t nfcore/cellranger:<VERSION>
+    ```
+
+4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
+
+    ```bash
     docker push nfcore/cellranger:<VERSION>
     ```

modules/cellranger/count/main.nf

@@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellranger:6.0.2"
+    container "nfcore/cellranger:6.1.2"
 
     input:
     tuple val(meta), path(reads)
@@ -15,6 +15,9 @@ process CELLRANGER_COUNT {
     path("sample-${meta.gem}/outs/*"), emit: outs
     path "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def sample_arg = meta.samples.unique().join(",")

modules/cellranger/mkfastq/Dockerfile

@@ -0,0 +1,40 @@
+# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
+# Push to nfcore/cellrangermkfastq:<VER>
+
+FROM continuumio/miniconda3:4.8.2
+LABEL authors="Regina Reynolds, Gisela Gabernet <gisela.gabernet@gmail.com>" \
+    description="Docker image containing bcl2fastq2 and Cell Ranger"
+# Disclaimer: this container is not provided nor supported by Illumina or 10x Genomics.
+
+# Install procps and clean apt cache
+RUN apt-get update --allow-releaseinfo-change \
+    && apt-get install -y \
+    cpio \
+    procps \
+    rpm2cpio \
+    unzip \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+# Copy pre-downloaded bcl2fastq2 and cellranger file
+ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
+    CELLRANGER_VER=6.1.2
+COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
+COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
+
+# Install bcl2fastq2
+RUN \
+    cd /tmp && \
+    unzip bcl2fastq2-$BCL2FASTQ2_VER.zip && \
+    mv *.rpm bcl2fastq2-$BCL2FASTQ2_VER.rpm && \
+    rpm2cpio ./bcl2fastq2-$BCL2FASTQ2_VER.rpm | cpio -idmv && \
+    export PATH=/tmp/usr/local/bin/:$PATH && \
+    ln -s /tmp/usr/local/bin/bcl2fastq /usr/bin/bcl2fastq && \
+    rm -rf bcl2fastq2-$BCL2FASTQ2_VER.*
+
+# Install cellranger
+RUN \
+    cd /opt && \
+    tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
+    export PATH=/opt/cellranger-$CELLRANGER_VER:$PATH && \
+    ln -s /opt/cellranger-$CELLRANGER_VER/cellranger /usr/bin/cellranger && \
+    rm -rf /opt/cellranger-$CELLRANGER_VER.tar.gz

modules/cellranger/mkfastq/README.md

@@ -0,0 +1,26 @@
+# Updating the docker container and making a new module release
+
+Bcl2fastq2 and Cell Ranger are commercial tools from Illumina and 10X Genomics, respectively. The container provided for the cellranger nf-core module is not provided nor supported by either Illumina or 10x Genomics. Updating the bcl2fastq2 or Cell Ranger versions in the container and pushing the update to Dockerhub needs to be done manually.
+
+1. Navigate to the appropriate download pages.
+        - [bcl2fastq2](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html): download the linux rpm installer of the desired bcl2fastq2 version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
+        - [Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest): download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
+
+2. Edit the Dockerfile. Update the bcl2fastq2 and Cell Ranger versions in this line:
+
+    ```bash
+    ENV BCL2FASTQ2_VER=<VERSION> \
+        CELLRANGER_VER=<VERSION>
+    ```
+
+3. Create and test the container:
+
+    ```bash
+    docker build . -t nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
+    ```
+
+4. Access rights are needed to push the container to the Dockerhub nfcore organization, please ask a core team member to do so.
+
+    ```bash
+    docker push nfcore/cellrangermkfastq:<CELLRANGER_VERSION>
+    ```

modules/cellranger/mkfastq/main.nf

@@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "litd/docker-cellranger:v6.1.1" // FIXME Add bcl2fastq to nf-core docker image
+    container "nfcore/cellrangermkfastq:6.1.2"
 
     input:
     path bcl
@@ -13,14 +13,17 @@ process CELLRANGER_MKFASTQ {
 
     output:
     path "versions.yml", emit: versions
-    path "*.fastq.gz"  , emit: fastq
+    path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz"  , emit: fastq
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     """
     cellranger mkfastq --id=${bcl.getSimpleName()} \
         --run=$bcl \
-        --csv=$csv
+        --csv=$csv \
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -28,4 +31,15 @@ process CELLRANGER_MKFASTQ {
         cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir -p "${bcl.getSimpleName()}/outs/fastq_path/"
+    touch ${bcl.getSimpleName()}/outs/fastq_path/fake_file.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
+    END_VERSIONS
+    """
 }

modules/cellranger/mkgtf/main.nf

@@ -5,7 +5,7 @@ process CELLRANGER_MKGTF {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellranger:6.0.2"
+    container "nfcore/cellranger:6.1.2"
 
     input:
     path gtf
@@ -14,6 +14,9 @@ process CELLRANGER_MKGTF {
     path "*.filtered.gtf", emit: gtf
     path "versions.yml"  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/cellranger/mkref/main.nf

@@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellranger:6.0.2"
+    container "nfcore/cellranger:6.1.2"
 
     input:
     path fasta
@@ -16,6 +16,9 @@ process CELLRANGER_MKREF {
     path "${reference_name}", emit: reference
     path "versions.yml"     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/checkm/lineagewf/main.nf

@@ -16,6 +16,9 @@ process CHECKM_LINEAGEWF {
     tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv
     path "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/chromap/chromap/main.nf

@@ -23,6 +23,9 @@ process CHROMAP_CHROMAP {
     tuple val(meta), path("*.pairs.gz")   , optional:true, emit: pairs
     path "versions.yml"                                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''

modules/chromap/index/main.nf

@@ -15,6 +15,9 @@ process CHROMAP_INDEX {
     path "*.index"     , emit: index
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = fasta.baseName

modules/clonalframeml/main.nf

@@ -19,6 +19,9 @@ process CLONALFRAMEML {
     tuple val(meta), path("*.position_cross_reference.txt"), emit: pos_ref
     path "versions.yml"                                    , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/cmseq/polymut/main.nf

@@ -16,6 +16,9 @@ process CMSEQ_POLYMUT {
     tuple val(meta), path("*.txt"), emit: polymut
     path "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/cnvkit/batch/main.nf

@@ -20,6 +20,9 @@ process CNVKIT_BATCH {
     tuple val(meta), path("*.cns"), emit: cns, optional: true
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def normal_args = normal ? "--normal $normal" : ""

modules/cooler/cload/main.nf

@@ -16,6 +16,9 @@ process COOLER_CLOAD {
     tuple val(meta), val(cool_bin), path("*.cool"), emit: cool
     path "versions.yml"                           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/cooler/digest/main.nf

@@ -16,6 +16,9 @@ process COOLER_DIGEST {
     path "*.bed"                  , emit: bed
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/cooler/dump/main.nf

@@ -15,6 +15,9 @@ process COOLER_DUMP {
     tuple val(meta), path("*.bedpe"), emit: bedpe
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/cooler/merge/main.nf

@@ -14,6 +14,9 @@ process COOLER_MERGE {
     tuple val(meta), path("*.cool"), emit: cool
     path "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/cooler/zoomify/main.nf

@@ -14,6 +14,9 @@ process COOLER_ZOOMIFY {
     tuple val(meta), path("*.mcool"), emit: mcool
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/csvtk/concat/main.nf

@@ -16,6 +16,9 @@ process CSVTK_CONCAT {
     tuple val(meta), path("${prefix}.${out_extension}"), emit: csv
     path "versions.yml"                                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/csvtk/split/main.nf

@@ -16,6 +16,9 @@ process CSVTK_SPLIT {
     tuple val(meta), path("*.${out_extension}"), emit: split_csv
     path "versions.yml"                        , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/custom/dumpsoftwareversions/main.nf

@@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     path "software_versions_mqc.yml", emit: mqc_yml
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     template 'dumpsoftwareversions.py'

modules/custom/getchromsizes/main.nf

@@ -15,6 +15,9 @@ process CUSTOM_GETCHROMSIZES {
     path '*.fai'        , emit: fai
     path  "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/cutadapt/main.nf

@@ -15,6 +15,9 @@ process CUTADAPT {
     tuple val(meta), path('*.log')          , emit: log
     path "versions.yml"                     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/damageprofiler/main.nf

@@ -17,6 +17,9 @@ process DAMAGEPROFILER {
     tuple val(meta), path("${prefix}"), emit: results
     path  "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/dastool/dastool/main.nf

@@ -26,6 +26,9 @@ process DASTOOL_DASTOOL {
     tuple val(meta), path("*.seqlength")                , optional: true, emit: seqlength
     path "versions.yml"                                 , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"