Merge branch 'maxquant' of github.com:veitveit/modules into maxquant

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

@@ -15,6 +15,9 @@ process BAMCMP {
     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}"

modules/bamtools/convert/main.nf

@@ -14,6 +14,9 @@ process BAMTOOLS_CONVERT {
     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}"

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

@@ -17,6 +17,9 @@ process BCFTOOLS_QUERY {
     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}"

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/count/main.nf

@@ -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/main.nf

@@ -15,6 +15,9 @@ process CELLRANGER_MKFASTQ {
     path "versions.yml", emit: versions
     path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz"  , emit: fastq
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """

modules/cellranger/mkgtf/main.nf

@@ -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

@@ -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}"

modules/dastool/scaffolds2bin/main.nf

@@ -15,6 +15,9 @@ process DASTOOL_SCAFFOLDS2BIN {
     tuple val(meta), path("*.tsv"), emit: scaffolds2bin
     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/dedup/main.nf

@@ -17,6 +17,9 @@ process DEDUP {
     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   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"

modules/deeparg/downloaddata/main.nf

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

modules/deeparg/predict/main.nf

@@ -20,6 +20,9 @@ process DEEPARG_PREDICT {
     tuple val(meta), path("*.mapping.potential.ARG"), emit: potential_arg
     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/deeptools/computematrix/main.nf

@@ -16,6 +16,9 @@ process DEEPTOOLS_COMPUTEMATRIX {
     tuple val(meta), path("*.mat.tab"), emit: table
     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/deeptools/plotfingerprint/main.nf

@@ -16,6 +16,9 @@ process DEEPTOOLS_PLOTFINGERPRINT {
     tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
     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/deeptools/plotheatmap/main.nf

@@ -15,6 +15,9 @@ process DEEPTOOLS_PLOTHEATMAP {
     tuple val(meta), path("*.tab"), emit: table
     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/deeptools/plotprofile/main.nf

@@ -15,6 +15,9 @@ process DEEPTOOLS_PLOTPROFILE {
     tuple val(meta), path("*.tab"), emit: table
     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/deepvariant/main.nf

@@ -21,6 +21,9 @@ process DEEPVARIANT {
     tuple val(meta), path("*g.vcf.gz"),  emit: gvcf
     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/delly/call/main.nf

@@ -17,6 +17,9 @@ process DELLY_CALL {
     tuple val(meta), path("*.csi"), emit: csi
     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}"