Add when: block

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}"