diff --git a/modules/abacas/main.nf b/modules/abacas/main.nf
index 49040214..00c9169f 100644
--- a/modules/abacas/main.nf
+++ b/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}"
diff --git a/modules/adapterremoval/main.nf b/modules/adapterremoval/main.nf
index 0cf257ff..55c5f17c 100644
--- a/modules/adapterremoval/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf
index aff72abc..8503505d 100644
--- a/modules/agrvate/main.nf
+++ b/modules/agrvate/main.nf
@@ -15,6 +15,9 @@ process AGRVATE {
     path "${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}"
diff --git a/modules/allelecounter/main.nf b/modules/allelecounter/main.nf
index 850a018f..b2cb1b0c 100644
--- a/modules/allelecounter/main.nf
+++ b/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}"
diff --git a/modules/amps/main.nf b/modules/amps/main.nf
index 871b57c6..57cdcff8 100644
--- a/modules/amps/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/arriba/main.nf b/modules/arriba/main.nf
index 0fcb6ba7..e0d30b45 100644
--- a/modules/arriba/main.nf
+++ b/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}"
diff --git a/modules/artic/guppyplex/main.nf b/modules/artic/guppyplex/main.nf
index 780f5111..8e6b2879 100644
--- a/modules/artic/guppyplex/main.nf
+++ b/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}"
diff --git a/modules/artic/minion/main.nf b/modules/artic/minion/main.nf
index c25ec0db..af74b132 100644
--- a/modules/artic/minion/main.nf
+++ b/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}"
diff --git a/modules/assemblyscan/main.nf b/modules/assemblyscan/main.nf
index 56541222..889f92a9 100644
--- a/modules/assemblyscan/main.nf
+++ b/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}"
diff --git a/modules/ataqv/ataqv/main.nf b/modules/ataqv/ataqv/main.nf
index fbd623f4..952aaed4 100644
--- a/modules/ataqv/ataqv/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/bakta/main.nf b/modules/bakta/main.nf
index 2582dac2..95e87899 100644
--- a/modules/bakta/main.nf
+++ b/modules/bakta/main.nf
@@ -25,6 +25,9 @@ process BAKTA {
     tuple val(meta), path("${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}"
diff --git a/modules/bamaligncleaner/main.nf b/modules/bamaligncleaner/main.nf
index 88fe21aa..922b72e6 100644
--- a/modules/bamaligncleaner/main.nf
+++ b/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}"
diff --git a/modules/bamcmp/main.nf b/modules/bamcmp/main.nf
index 54416323..f45b73d8 100644
--- a/modules/bamcmp/main.nf
+++ b/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}"
diff --git a/modules/bamtools/convert/main.nf b/modules/bamtools/convert/main.nf
index 141e762d..b993aad1 100644
--- a/modules/bamtools/convert/main.nf
+++ b/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}"
diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 8d5e5690..014e5cdb 100644
--- a/modules/bamtools/split/main.nf
+++ b/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}"
diff --git a/modules/bamutil/trimbam/main.nf b/modules/bamutil/trimbam/main.nf
index 9ceb2b65..514ea4c0 100644
--- a/modules/bamutil/trimbam/main.nf
+++ b/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}"
diff --git a/modules/bandage/image/main.nf b/modules/bandage/image/main.nf
index bc2a9495..ee504a12 100644
--- a/modules/bandage/image/main.nf
+++ b/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}"
diff --git a/modules/bbmap/align/main.nf b/modules/bbmap/align/main.nf
index ac839497..914399c5 100644
--- a/modules/bbmap/align/main.nf
+++ b/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}"
diff --git a/modules/bbmap/bbduk/main.nf b/modules/bbmap/bbduk/main.nf
index 79c3c306..0ae005e4 100644
--- a/modules/bbmap/bbduk/main.nf
+++ b/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}"
diff --git a/modules/bbmap/bbsplit/main.nf b/modules/bbmap/bbsplit/main.nf
index 0c916dfe..b55929ce 100644
--- a/modules/bbmap/bbsplit/main.nf
+++ b/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}"
diff --git a/modules/bbmap/index/main.nf b/modules/bbmap/index/main.nf
index 4c02f84e..fdd6d102 100644
--- a/modules/bbmap/index/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf
index d02e7605..c0633ef7 100644
--- a/modules/bcftools/concat/main.nf
+++ b/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}"
diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf
index 040e6534..a0c436e2 100644
--- a/modules/bcftools/consensus/main.nf
+++ b/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}"
diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf
index 98b422b1..82961e32 100644
--- a/modules/bcftools/filter/main.nf
+++ b/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}"
diff --git a/modules/bcftools/index/main.nf b/modules/bcftools/index/main.nf
index e5275003..548a9277 100644
--- a/modules/bcftools/index/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf
index fdde3022..c8f89753 100644
--- a/modules/bcftools/isec/main.nf
+++ b/modules/bcftools/isec/main.nf
@@ -14,6 +14,9 @@ process BCFTOOLS_ISEC {
     tuple val(meta), path("${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}"
diff --git a/modules/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf
index f1c02e8d..7bee5a9b 100644
--- a/modules/bcftools/merge/main.nf
+++ b/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}"
diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf
index cdd38eec..676eae7a 100644
--- a/modules/bcftools/mpileup/main.nf
+++ b/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 ?: ''
diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf
index e8bf6324..cd681f21 100644
--- a/modules/bcftools/norm/main.nf
+++ b/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}"
diff --git a/modules/bcftools/query/main.nf b/modules/bcftools/query/main.nf
index a165b103..8921abdd 100644
--- a/modules/bcftools/query/main.nf
+++ b/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}"
diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf
index e6d9025d..7d2abecf 100644
--- a/modules/bcftools/reheader/main.nf
+++ b/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}"
diff --git a/modules/bcftools/sort/main.nf b/modules/bcftools/sort/main.nf
index 2fcadc98..8478fe25 100644
--- a/modules/bcftools/sort/main.nf
+++ b/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}"
diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf
index 54a28bce..7e150d1f 100644
--- a/modules/bcftools/stats/main.nf
+++ b/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}"
diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf
index 7056ecdb..2a240f4a 100644
--- a/modules/bcftools/view/main.nf
+++ b/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}"
diff --git a/modules/bedtools/bamtobed/main.nf b/modules/bedtools/bamtobed/main.nf
index 98d9ea2f..fd782dec 100644
--- a/modules/bedtools/bamtobed/main.nf
+++ b/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}"
diff --git a/modules/bedtools/complement/main.nf b/modules/bedtools/complement/main.nf
index 3146827c..8c8e7efa 100644
--- a/modules/bedtools/complement/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/bedtools/genomecov/main.nf b/modules/bedtools/genomecov/main.nf
index ca491e75..4804d40a 100644
--- a/modules/bedtools/genomecov/main.nf
+++ b/modules/bedtools/genomecov/main.nf
@@ -16,6 +16,9 @@ process BEDTOOLS_GENOMECOV {
     tuple val(meta), path("*.${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()
diff --git a/modules/bedtools/getfasta/main.nf b/modules/bedtools/getfasta/main.nf
index 5a283e94..4ce8c01e 100644
--- a/modules/bedtools/getfasta/main.nf
+++ b/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 ?: "${bed.baseName}"
diff --git a/modules/bedtools/intersect/main.nf b/modules/bedtools/intersect/main.nf
index afb0d056..29f16adb 100644
--- a/modules/bedtools/intersect/main.nf
+++ b/modules/bedtools/intersect/main.nf
@@ -15,6 +15,9 @@ process BEDTOOLS_INTERSECT {
     tuple val(meta), path("*.${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}"
diff --git a/modules/bedtools/makewindows/main.nf b/modules/bedtools/makewindows/main.nf
index 2414393c..2a19226c 100644
--- a/modules/bedtools/makewindows/main.nf
+++ b/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}"
diff --git a/modules/bedtools/maskfasta/main.nf b/modules/bedtools/maskfasta/main.nf
index 7eeb4c7d..04ba116b 100644
--- a/modules/bedtools/maskfasta/main.nf
+++ b/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}"
diff --git a/modules/bedtools/merge/main.nf b/modules/bedtools/merge/main.nf
index 5f1da95b..6d1daa03 100644
--- a/modules/bedtools/merge/main.nf
+++ b/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}"
diff --git a/modules/bedtools/slop/main.nf b/modules/bedtools/slop/main.nf
index 9d8633ec..ae4f81cc 100644
--- a/modules/bedtools/slop/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf
index 1ed95a57..43dc9bda 100644
--- a/modules/bedtools/sort/main.nf
+++ b/modules/bedtools/sort/main.nf
@@ -15,6 +15,9 @@ process BEDTOOLS_SORT {
     tuple val(meta), path("*.${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}"
diff --git a/modules/bedtools/subtract/main.nf b/modules/bedtools/subtract/main.nf
index b2efefe5..8e2b42c5 100644
--- a/modules/bedtools/subtract/main.nf
+++ b/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}"
diff --git a/modules/bismark/align/main.nf b/modules/bismark/align/main.nf
index e490b48c..eeddcabb 100644
--- a/modules/bismark/align/main.nf
+++ b/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}"
diff --git a/modules/bismark/deduplicate/main.nf b/modules/bismark/deduplicate/main.nf
index 16c624f1..ea763774 100644
--- a/modules/bismark/deduplicate/main.nf
+++ b/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}"
diff --git a/modules/bismark/genomepreparation/main.nf b/modules/bismark/genomepreparation/main.nf
index e096b2b8..59c495c5 100644
--- a/modules/bismark/genomepreparation/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bismark/methylationextractor/main.nf b/modules/bismark/methylationextractor/main.nf
index d99c2b5e..5543ab7e 100644
--- a/modules/bismark/methylationextractor/main.nf
+++ b/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'
diff --git a/modules/bismark/report/main.nf b/modules/bismark/report/main.nf
index f828ecd8..bec3de99 100644
--- a/modules/bismark/report/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bismark/summary/main.nf b/modules/bismark/summary/main.nf
index 72dba72e..49fec53e 100644
--- a/modules/bismark/summary/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/blast/blastn/main.nf b/modules/blast/blastn/main.nf
index 3a0bafe0..b85f6c8e 100644
--- a/modules/blast/blastn/main.nf
+++ b/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}"
diff --git a/modules/blast/makeblastdb/main.nf b/modules/blast/makeblastdb/main.nf
index b4c426a4..12208ea8 100644
--- a/modules/blast/makeblastdb/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bowtie/align/main.nf b/modules/bowtie/align/main.nf
index b25b5e21..ba82b67d 100644
--- a/modules/bowtie/align/main.nf
+++ b/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 ?: ''
diff --git a/modules/bowtie/build/main.nf b/modules/bowtie/build/main.nf
index dbbc8efa..e01d9855 100644
--- a/modules/bowtie/build/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 20b08f72..7e8a9659 100644
--- a/modules/bowtie2/align/main.nf
+++ b/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 ?: ''
diff --git a/modules/bowtie2/build/main.nf b/modules/bowtie2/build/main.nf
index da2e9ed5..a4da62d0 100644
--- a/modules/bowtie2/build/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bwa/aln/main.nf b/modules/bwa/aln/main.nf
index 992e25de..741c0159 100644
--- a/modules/bwa/aln/main.nf
+++ b/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}"
diff --git a/modules/bwa/index/main.nf b/modules/bwa/index/main.nf
index 89102737..3affbf16 100644
--- a/modules/bwa/index/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bwa/mem/main.nf b/modules/bwa/mem/main.nf
index 9695bd2d..9a91c77f 100644
--- a/modules/bwa/mem/main.nf
+++ b/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 ?: ''
diff --git a/modules/bwa/sampe/main.nf b/modules/bwa/sampe/main.nf
index 0b5ec255..e781679e 100644
--- a/modules/bwa/sampe/main.nf
+++ b/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}"
diff --git a/modules/bwa/samse/main.nf b/modules/bwa/samse/main.nf
index bee06bc8..ac04c739 100644
--- a/modules/bwa/samse/main.nf
+++ b/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}"
diff --git a/modules/bwamem2/index/main.nf b/modules/bwamem2/index/main.nf
index e00538c9..0e9cc2f8 100644
--- a/modules/bwamem2/index/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/bwamem2/mem/main.nf b/modules/bwamem2/mem/main.nf
index 6d4d8028..56f595ec 100644
--- a/modules/bwamem2/mem/main.nf
+++ b/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 ?: ''
diff --git a/modules/bwameth/align/main.nf b/modules/bwameth/align/main.nf
index 0bcd9bac..6d9c4431 100644
--- a/modules/bwameth/align/main.nf
+++ b/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 ?: ''
diff --git a/modules/bwameth/index/main.nf b/modules/bwameth/index/main.nf
index f5b8ff59..4c106826 100644
--- a/modules/bwameth/index/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/cat/cat/main.nf b/modules/cat/cat/main.nf
index 2efe20a5..4ee44599 100644
--- a/modules/cat/cat/main.nf
+++ b/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 ?: ''
diff --git a/modules/cat/fastq/main.nf b/modules/cat/fastq/main.nf
index d02598e1..bf0877c3 100644
--- a/modules/cat/fastq/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/cellranger/count/main.nf b/modules/cellranger/count/main.nf
index 63fac709..6a206b6e 100644
--- a/modules/cellranger/count/main.nf
+++ b/modules/cellranger/count/main.nf
@@ -15,6 +15,9 @@ process CELLRANGER_COUNT {
     path("sample-${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(",")
diff --git a/modules/cellranger/mkfastq/main.nf b/modules/cellranger/mkfastq/main.nf
index f47aa75c..9c023bca 100644
--- a/modules/cellranger/mkfastq/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/cellranger/mkgtf/main.nf b/modules/cellranger/mkgtf/main.nf
index 4342fd00..9dc2fe1a 100644
--- a/modules/cellranger/mkgtf/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/cellranger/mkref/main.nf b/modules/cellranger/mkref/main.nf
index d38d6809..11cf80e3 100644
--- a/modules/cellranger/mkref/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/checkm/lineagewf/main.nf b/modules/checkm/lineagewf/main.nf
index 992b165e..d92f2c78 100644
--- a/modules/checkm/lineagewf/main.nf
+++ b/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}"
diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf
index 67384b0c..cdbf6049 100644
--- a/modules/chromap/chromap/main.nf
+++ b/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 ?: ''
diff --git a/modules/chromap/index/main.nf b/modules/chromap/index/main.nf
index 61bcee10..52deaf06 100644
--- a/modules/chromap/index/main.nf
+++ b/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
diff --git a/modules/clonalframeml/main.nf b/modules/clonalframeml/main.nf
index db647a38..24502796 100644
--- a/modules/clonalframeml/main.nf
+++ b/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}"
diff --git a/modules/cmseq/polymut/main.nf b/modules/cmseq/polymut/main.nf
index 47e86f0c..a02551c8 100644
--- a/modules/cmseq/polymut/main.nf
+++ b/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}"
diff --git a/modules/cnvkit/batch/main.nf b/modules/cnvkit/batch/main.nf
index 811cb409..7c44d9f6 100644
--- a/modules/cnvkit/batch/main.nf
+++ b/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" : ""
diff --git a/modules/cooler/cload/main.nf b/modules/cooler/cload/main.nf
index d8bdc031..52964b8d 100644
--- a/modules/cooler/cload/main.nf
+++ b/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}"
diff --git a/modules/cooler/digest/main.nf b/modules/cooler/digest/main.nf
index 9658ec31..7e8e36f0 100644
--- a/modules/cooler/digest/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/cooler/dump/main.nf b/modules/cooler/dump/main.nf
index a438acc8..996e9b5b 100644
--- a/modules/cooler/dump/main.nf
+++ b/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}"
diff --git a/modules/cooler/merge/main.nf b/modules/cooler/merge/main.nf
index b1814b68..1e439caf 100644
--- a/modules/cooler/merge/main.nf
+++ b/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}"
diff --git a/modules/cooler/zoomify/main.nf b/modules/cooler/zoomify/main.nf
index 226d4114..942282c0 100644
--- a/modules/cooler/zoomify/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/csvtk/concat/main.nf b/modules/csvtk/concat/main.nf
index 94b1925a..f30e8332 100644
--- a/modules/csvtk/concat/main.nf
+++ b/modules/csvtk/concat/main.nf
@@ -16,6 +16,9 @@ process CSVTK_CONCAT {
     tuple val(meta), path("${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 ?: "${meta.id}"
diff --git a/modules/csvtk/split/main.nf b/modules/csvtk/split/main.nf
index 52ab7ec7..5653d192 100644
--- a/modules/csvtk/split/main.nf
+++ b/modules/csvtk/split/main.nf
@@ -16,6 +16,9 @@ process CSVTK_SPLIT {
     tuple val(meta), path("*.${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}"
diff --git a/modules/custom/dumpsoftwareversions/main.nf b/modules/custom/dumpsoftwareversions/main.nf
index 934bb467..327d5100 100644
--- a/modules/custom/dumpsoftwareversions/main.nf
+++ b/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'
diff --git a/modules/custom/getchromsizes/main.nf b/modules/custom/getchromsizes/main.nf
index 270b3f48..39da7d34 100644
--- a/modules/custom/getchromsizes/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/cutadapt/main.nf b/modules/cutadapt/main.nf
index 74c42768..9b310c0e 100644
--- a/modules/cutadapt/main.nf
+++ b/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 ?: "${meta.id}"
diff --git a/modules/damageprofiler/main.nf b/modules/damageprofiler/main.nf
index 23eb9397..4b146e7f 100644
--- a/modules/damageprofiler/main.nf
+++ b/modules/damageprofiler/main.nf
@@ -17,6 +17,9 @@ process DAMAGEPROFILER {
     tuple val(meta), path("${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}"
diff --git a/modules/dastool/dastool/main.nf b/modules/dastool/dastool/main.nf
index 722f6c55..53dfea19 100644
--- a/modules/dastool/dastool/main.nf
+++ b/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}"
diff --git a/modules/dastool/scaffolds2bin/main.nf b/modules/dastool/scaffolds2bin/main.nf
index 09f800bb..6e9fcdc2 100644
--- a/modules/dastool/scaffolds2bin/main.nf
+++ b/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}"
diff --git a/modules/dedup/main.nf b/modules/dedup/main.nf
index 8b4bdc37..c612ec14 100644
--- a/modules/dedup/main.nf
+++ b/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}"
diff --git a/modules/deeparg/downloaddata/main.nf b/modules/deeparg/downloaddata/main.nf
index cc420e6a..aacdc778 100644
--- a/modules/deeparg/downloaddata/main.nf
+++ b/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 ?: ''
     """
diff --git a/modules/deeparg/predict/main.nf b/modules/deeparg/predict/main.nf
index 9408fa3d..3e478e59 100644
--- a/modules/deeparg/predict/main.nf
+++ b/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}"
diff --git a/modules/deeptools/computematrix/main.nf b/modules/deeptools/computematrix/main.nf
index 70be934b..96dfef3c 100644
--- a/modules/deeptools/computematrix/main.nf
+++ b/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}"
diff --git a/modules/deeptools/plotfingerprint/main.nf b/modules/deeptools/plotfingerprint/main.nf
index 7925c9a9..83613be7 100644
--- a/modules/deeptools/plotfingerprint/main.nf
+++ b/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}"
diff --git a/modules/deeptools/plotheatmap/main.nf b/modules/deeptools/plotheatmap/main.nf
index 992c9058..1e402e39 100644
--- a/modules/deeptools/plotheatmap/main.nf
+++ b/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}"
diff --git a/modules/deeptools/plotprofile/main.nf b/modules/deeptools/plotprofile/main.nf
index 60184fa6..d83a9493 100644
--- a/modules/deeptools/plotprofile/main.nf
+++ b/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}"
diff --git a/modules/deepvariant/main.nf b/modules/deepvariant/main.nf
index 98345c83..c5e81997 100644
--- a/modules/deepvariant/main.nf
+++ b/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}"
diff --git a/modules/delly/call/main.nf b/modules/delly/call/main.nf
index fc04cda7..d639ee16 100644
--- a/modules/delly/call/main.nf
+++ b/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}"
diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index c7342767..955952dc 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -17,6 +17,9 @@ process DIAMOND_BLASTP {
     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}"
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index bd7d1dd9..3700bd36 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -17,6 +17,9 @@ process DIAMOND_BLASTX {
     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 ?: "${meta.id}"
diff --git a/modules/diamond/makedb/main.nf b/modules/diamond/makedb/main.nf
index cccfcce9..e3d62f00 100644
--- a/modules/diamond/makedb/main.nf
+++ b/modules/diamond/makedb/main.nf
@@ -16,6 +16,9 @@ process DIAMOND_MAKEDB {
     path "${fasta}.dmnd", emit: db
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/dragmap/align/main.nf b/modules/dragmap/align/main.nf
index 8a6f082a..9f261cc2 100644
--- a/modules/dragmap/align/main.nf
+++ b/modules/dragmap/align/main.nf
@@ -17,6 +17,9 @@ process DRAGMAP_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 args2 = task.ext.args2 ?: ''
diff --git a/modules/dragmap/hashtable/main.nf b/modules/dragmap/hashtable/main.nf
index ab55364b..81333dfd 100644
--- a/modules/dragmap/hashtable/main.nf
+++ b/modules/dragmap/hashtable/main.nf
@@ -14,6 +14,9 @@ process DRAGMAP_HASHTABLE {
     path "dragmap"      , emit: hashmap
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/dragonflye/main.nf b/modules/dragonflye/main.nf
index 8ca98832..14597143 100644
--- a/modules/dragonflye/main.nf
+++ b/modules/dragonflye/main.nf
@@ -18,6 +18,9 @@ process DRAGONFLYE {
     tuple val(meta), path("flye-info.txt"), optional:true                      , emit: txt
     path "versions.yml"                                                        , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def memory = task.memory.toGiga()
diff --git a/modules/dshbio/exportsegments/main.nf b/modules/dshbio/exportsegments/main.nf
index 0a1920a6..49442f81 100644
--- a/modules/dshbio/exportsegments/main.nf
+++ b/modules/dshbio/exportsegments/main.nf
@@ -14,6 +14,9 @@ process DSHBIO_EXPORTSEGMENTS {
     tuple val(meta), path("*.fa.gz"), 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}"
diff --git a/modules/dshbio/filterbed/main.nf b/modules/dshbio/filterbed/main.nf
index 6efe07e8..7e3da24e 100644
--- a/modules/dshbio/filterbed/main.nf
+++ b/modules/dshbio/filterbed/main.nf
@@ -14,6 +14,9 @@ process DSHBIO_FILTERBED {
     tuple val(meta), path("*.bed.gz"), 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}"
diff --git a/modules/dshbio/filtergff3/main.nf b/modules/dshbio/filtergff3/main.nf
index 5214ce23..0539bbe0 100644
--- a/modules/dshbio/filtergff3/main.nf
+++ b/modules/dshbio/filtergff3/main.nf
@@ -14,6 +14,9 @@ process DSHBIO_FILTERGFF3 {
     tuple val(meta), path("*.gff3.gz"), emit: gff3
     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}"
diff --git a/modules/dshbio/splitbed/main.nf b/modules/dshbio/splitbed/main.nf
index c0ca6a8b..824c7e4d 100644
--- a/modules/dshbio/splitbed/main.nf
+++ b/modules/dshbio/splitbed/main.nf
@@ -14,6 +14,9 @@ process DSHBIO_SPLITBED {
     tuple val(meta), path("*.bed.gz"), 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}"
diff --git a/modules/dshbio/splitgff3/main.nf b/modules/dshbio/splitgff3/main.nf
index 012afec7..424bc368 100644
--- a/modules/dshbio/splitgff3/main.nf
+++ b/modules/dshbio/splitgff3/main.nf
@@ -14,6 +14,9 @@ process DSHBIO_SPLITGFF3 {
     tuple val(meta), path("*.gff3.gz"), emit: gff3
     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}"
diff --git a/modules/ectyper/main.nf b/modules/ectyper/main.nf
index 0e040958..34973ee6 100644
--- a/modules/ectyper/main.nf
+++ b/modules/ectyper/main.nf
@@ -16,6 +16,9 @@ process ECTYPER {
     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}"
diff --git a/modules/emmtyper/main.nf b/modules/emmtyper/main.nf
index 70dabfb7..955cc308 100644
--- a/modules/emmtyper/main.nf
+++ b/modules/emmtyper/main.nf
@@ -14,6 +14,9 @@ process EMMTYPER {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf
index e3d0c286..c2bd055f 100644
--- a/modules/ensemblvep/main.nf
+++ b/modules/ensemblvep/main.nf
@@ -19,6 +19,9 @@ process ENSEMBLVEP {
     path "*.summary.html"             , 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}"
diff --git a/modules/expansionhunter/main.nf b/modules/expansionhunter/main.nf
index 4db78230..4e62b2a6 100644
--- a/modules/expansionhunter/main.nf
+++ b/modules/expansionhunter/main.nf
@@ -16,6 +16,9 @@ process EXPANSIONHUNTER {
     tuple val(meta), path("*.vcf"), 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 ?: "${meta.id}"
diff --git a/modules/fargene/main.nf b/modules/fargene/main.nf
index 73bdd411..029f6065 100644
--- a/modules/fargene/main.nf
+++ b/modules/fargene/main.nf
@@ -31,6 +31,9 @@ process FARGENE {
     tuple val(meta), path("${prefix}/tmpdir/*.out")                                              , optional: true, emit: tmp
     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}"
diff --git a/modules/fastani/main.nf b/modules/fastani/main.nf
index cc1c4902..e6b44a82 100644
--- a/modules/fastani/main.nf
+++ b/modules/fastani/main.nf
@@ -15,6 +15,9 @@ process FASTANI {
     tuple val(meta), path("*.ani.txt"), emit: ani
     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}"
diff --git a/modules/fastp/main.nf b/modules/fastp/main.nf
index a406036a..d8218350 100644
--- a/modules/fastp/main.nf
+++ b/modules/fastp/main.nf
@@ -21,6 +21,9 @@ process FASTP {
     tuple val(meta), path('*.fail.fastq.gz')  , optional:true, emit: reads_fail
     tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     // Added soft-links to original fastqs for consistent naming in MultiQC
diff --git a/modules/fastqc/main.nf b/modules/fastqc/main.nf
index d250eca0..ed6b8c50 100644
--- a/modules/fastqc/main.nf
+++ b/modules/fastqc/main.nf
@@ -15,6 +15,9 @@ process FASTQC {
     tuple val(meta), path("*.zip") , emit: zip
     path  "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     // Add soft-links to original FastQs for consistent naming in pipeline
diff --git a/modules/fastqscan/main.nf b/modules/fastqscan/main.nf
index a0dcc46a..4cca0317 100644
--- a/modules/fastqscan/main.nf
+++ b/modules/fastqscan/main.nf
@@ -14,6 +14,9 @@ process FASTQSCAN {
     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}"
diff --git a/modules/fasttree/main.nf b/modules/fasttree/main.nf
index 5e57aae9..ce65846a 100644
--- a/modules/fasttree/main.nf
+++ b/modules/fasttree/main.nf
@@ -13,6 +13,9 @@ process FASTTREE {
     path "*.tre",         emit: phylogeny
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/fgbio/callmolecularconsensusreads/main.nf
index 3aab935b..347dc269 100644
--- a/modules/fgbio/callmolecularconsensusreads/main.nf
+++ b/modules/fgbio/callmolecularconsensusreads/main.nf
@@ -14,6 +14,9 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
     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}"
diff --git a/modules/fgbio/fastqtobam/main.nf b/modules/fgbio/fastqtobam/main.nf
index 3060d715..329aff33 100644
--- a/modules/fgbio/fastqtobam/main.nf
+++ b/modules/fgbio/fastqtobam/main.nf
@@ -15,6 +15,9 @@ process FGBIO_FASTQTOBAM {
     tuple val(meta), path("*_umi_converted.bam"), emit: umibam
     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}"
diff --git a/modules/fgbio/groupreadsbyumi/main.nf b/modules/fgbio/groupreadsbyumi/main.nf
index 47f000a5..31250d23 100644
--- a/modules/fgbio/groupreadsbyumi/main.nf
+++ b/modules/fgbio/groupreadsbyumi/main.nf
@@ -16,6 +16,9 @@ process FGBIO_GROUPREADSBYUMI {
     tuple val(meta), path("*_umi_histogram.txt"), emit: histogram
     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}"
diff --git a/modules/fgbio/sortbam/main.nf b/modules/fgbio/sortbam/main.nf
index c542f3df..5026987c 100644
--- a/modules/fgbio/sortbam/main.nf
+++ b/modules/fgbio/sortbam/main.nf
@@ -14,6 +14,9 @@ process FGBIO_SORTBAM {
     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 ?: "${meta.id}"
diff --git a/modules/filtlong/main.nf b/modules/filtlong/main.nf
index bb1c1eb3..0e6fdd53 100644
--- a/modules/filtlong/main.nf
+++ b/modules/filtlong/main.nf
@@ -14,6 +14,9 @@ process FILTLONG {
     tuple val(meta), path("${meta.id}_lr_filtlong.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}"
diff --git a/modules/flash/main.nf b/modules/flash/main.nf
index 7bc38c97..bb6f2499 100644
--- a/modules/flash/main.nf
+++ b/modules/flash/main.nf
@@ -13,6 +13,9 @@ process FLASH {
     tuple val(meta), path("*.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}"
diff --git a/modules/freebayes/main.nf b/modules/freebayes/main.nf
index d462088a..e67e4c72 100644
--- a/modules/freebayes/main.nf
+++ b/modules/freebayes/main.nf
@@ -20,6 +20,9 @@ process FREEBAYES {
     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}"
diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf
index c246190a..672e93e0 100644
--- a/modules/gatk4/applybqsr/main.nf
+++ b/modules/gatk4/applybqsr/main.nf
@@ -18,6 +18,9 @@ process GATK4_APPLYBQSR {
     tuple val(meta), path("*.cram"), emit: cram, 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}"
diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf
index 99233975..006840b3 100644
--- a/modules/gatk4/applyvqsr/main.nf
+++ b/modules/gatk4/applyvqsr/main.nf
@@ -21,6 +21,9 @@ process GATK4_APPLYVQSR {
     tuple val(meta), path("*.tbi")        , 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}"
diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf
index 42391d62..48c127f0 100644
--- a/modules/gatk4/baserecalibrator/main.nf
+++ b/modules/gatk4/baserecalibrator/main.nf
@@ -19,6 +19,9 @@ process GATK4_BASERECALIBRATOR {
     tuple val(meta), path("*.table"), 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}"
diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf
index 37f46f48..9f2b2dfe 100644
--- a/modules/gatk4/bedtointervallist/main.nf
+++ b/modules/gatk4/bedtointervallist/main.nf
@@ -15,6 +15,9 @@ process GATK4_BEDTOINTERVALLIST {
     tuple val(meta), path('*.interval_list'), emit: interval_list
     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}"
diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf
index f4e98f64..177f4878 100644
--- a/modules/gatk4/calculatecontamination/main.nf
+++ b/modules/gatk4/calculatecontamination/main.nf
@@ -16,6 +16,9 @@ process GATK4_CALCULATECONTAMINATION {
     tuple val(meta), path('*.segmentation.table') , emit: segmentation, 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}"
diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf
index 2cbd8948..714843c2 100644
--- a/modules/gatk4/createsequencedictionary/main.nf
+++ b/modules/gatk4/createsequencedictionary/main.nf
@@ -14,6 +14,9 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     path "*.dict"        , emit: dict
     path "versions.yml"  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 6
diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf
index 8ab578c4..a82c24d8 100644
--- a/modules/gatk4/createsomaticpanelofnormals/main.nf
+++ b/modules/gatk4/createsomaticpanelofnormals/main.nf
@@ -18,6 +18,9 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
     tuple val(meta), path("*.tbi")   , 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}"
diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf
index 744ebf21..2894e305 100644
--- a/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ b/modules/gatk4/estimatelibrarycomplexity/main.nf
@@ -17,6 +17,9 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
     tuple val(meta), path('*.metrics'), 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}"
diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf
index f0116b41..631c0394 100644
--- a/modules/gatk4/fastqtosam/main.nf
+++ b/modules/gatk4/fastqtosam/main.nf
@@ -14,6 +14,9 @@ process GATK4_FASTQTOSAM {
     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}"
diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf
index 2f5f8dcb..a7dd9a61 100644
--- a/modules/gatk4/filtermutectcalls/main.nf
+++ b/modules/gatk4/filtermutectcalls/main.nf
@@ -19,6 +19,9 @@ process GATK4_FILTERMUTECTCALLS {
     tuple val(meta), path("*.filteringStats.tsv"), 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}"
diff --git a/modules/gatk4/gatherbqsrreports/main.nf b/modules/gatk4/gatherbqsrreports/main.nf
index b084ab00..f8d91a92 100644
--- a/modules/gatk4/gatherbqsrreports/main.nf
+++ b/modules/gatk4/gatherbqsrreports/main.nf
@@ -14,6 +14,9 @@ process GATK4_GATHERBQSRREPORTS {
     tuple val(meta), path("*.table"), 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}"
diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf
index 94a589cd..e88471e1 100644
--- a/modules/gatk4/genomicsdbimport/main.nf
+++ b/modules/gatk4/genomicsdbimport/main.nf
@@ -19,6 +19,9 @@ process GATK4_GENOMICSDBIMPORT {
     tuple val(meta), path("*.interval_list"), optional:true, emit: intervallist
     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}"
diff --git a/modules/gatk4/genotypegvcfs/main.nf b/modules/gatk4/genotypegvcfs/main.nf
index 016da1f5..c3e41229 100644
--- a/modules/gatk4/genotypegvcfs/main.nf
+++ b/modules/gatk4/genotypegvcfs/main.nf
@@ -20,6 +20,9 @@ process GATK4_GENOTYPEGVCFS {
     tuple val(meta), path("*.tbi")   , 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}"
diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf
index a81ae635..3667a210 100644
--- a/modules/gatk4/getpileupsummaries/main.nf
+++ b/modules/gatk4/getpileupsummaries/main.nf
@@ -17,6 +17,9 @@ process GATK4_GETPILEUPSUMMARIES {
     tuple val(meta), path('*.pileups.table'), 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}"
diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf
index 8c22da68..6f03ffd2 100644
--- a/modules/gatk4/haplotypecaller/main.nf
+++ b/modules/gatk4/haplotypecaller/main.nf
@@ -20,6 +20,9 @@ process GATK4_HAPLOTYPECALLER {
     tuple val(meta), path("*.tbi")   , 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}"
diff --git a/modules/gatk4/indexfeaturefile/main.nf b/modules/gatk4/indexfeaturefile/main.nf
index ecd24173..b5add0e0 100644
--- a/modules/gatk4/indexfeaturefile/main.nf
+++ b/modules/gatk4/indexfeaturefile/main.nf
@@ -14,6 +14,9 @@ process GATK4_INDEXFEATUREFILE {
     tuple val(meta), path("*.{tbi,idx}"), emit: index
     path  "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 3
diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf
index 17412160..40c7fb19 100644
--- a/modules/gatk4/intervallisttools/main.nf
+++ b/modules/gatk4/intervallisttools/main.nf
@@ -14,6 +14,9 @@ process GATK4_INTERVALLISTTOOLS {
     tuple val(meta), path("*_split/*/*.interval_list"), emit: interval_list
     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}"
diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf
index d1bce19f..7d96c27e 100644
--- a/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/modules/gatk4/learnreadorientationmodel/main.nf
@@ -14,6 +14,9 @@ process GATK4_LEARNREADORIENTATIONMODEL {
     tuple val(meta), path("*.tar.gz"), emit: artifactprior
     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}"
diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf
index c101d042..735b093e 100644
--- a/modules/gatk4/markduplicates/main.nf
+++ b/modules/gatk4/markduplicates/main.nf
@@ -16,6 +16,9 @@ process GATK4_MARKDUPLICATES {
     tuple val(meta), path("*.metrics"), 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}"
diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf
index 0e294454..e636e1cd 100644
--- a/modules/gatk4/mergebamalignment/main.nf
+++ b/modules/gatk4/mergebamalignment/main.nf
@@ -16,6 +16,9 @@ process GATK4_MERGEBAMALIGNMENT {
     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}"
diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf
index b2e584a8..3e9973e7 100644
--- a/modules/gatk4/mergevcfs/main.nf
+++ b/modules/gatk4/mergevcfs/main.nf
@@ -16,6 +16,9 @@ process GATK4_MERGEVCFS {
     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}"
diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index c33cee18..1c8c3993 100644
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@@ -28,6 +28,9 @@ process GATK4_MUTECT2 {
     tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2
     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}"
diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 5a13d61d..23f99ab4 100644
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@@ -14,6 +14,9 @@ process GATK4_REVERTSAM {
     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}"
diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf
index 0a75f604..2da40b6c 100644
--- a/modules/gatk4/samtofastq/main.nf
+++ b/modules/gatk4/samtofastq/main.nf
@@ -14,6 +14,9 @@ process GATK4_SAMTOFASTQ {
     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}"
diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index 29483fb5..6d0a35fd 100644
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@@ -17,6 +17,9 @@ process GATK4_SPLITNCIGARREADS {
     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}"
diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf
index beaec0c0..3a41d20c 100644
--- a/modules/gatk4/variantfiltration/main.nf
+++ b/modules/gatk4/variantfiltration/main.nf
@@ -18,6 +18,9 @@ process GATK4_VARIANTFILTRATION {
     tuple val(meta), path("*.tbi")   , 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}"
diff --git a/modules/gatk4/variantrecalibrator/main.nf b/modules/gatk4/variantrecalibrator/main.nf
index c4aa5535..df8a9599 100644
--- a/modules/gatk4/variantrecalibrator/main.nf
+++ b/modules/gatk4/variantrecalibrator/main.nf
@@ -25,6 +25,9 @@ process GATK4_VARIANTRECALIBRATOR {
     tuple val(meta), path("*plots.R")  , emit: plots, 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}"
diff --git a/modules/genmap/index/main.nf b/modules/genmap/index/main.nf
index 943f1a31..a19c6619 100644
--- a/modules/genmap/index/main.nf
+++ b/modules/genmap/index/main.nf
@@ -14,6 +14,9 @@ process GENMAP_INDEX {
     path "genmap"       , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/genmap/mappability/main.nf b/modules/genmap/mappability/main.nf
index 94083f14..50a17493 100644
--- a/modules/genmap/mappability/main.nf
+++ b/modules/genmap/mappability/main.nf
@@ -16,6 +16,9 @@ process GENMAP_MAPPABILITY {
     path "*.txt"        , optional:true, emit: txt
     path "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/genrich/main.nf b/modules/genrich/main.nf
index d9deea3c..d276c410 100644
--- a/modules/genrich/main.nf
+++ b/modules/genrich/main.nf
@@ -24,6 +24,9 @@ process GENRICH {
     tuple val(meta), path("*duplicates.txt")  , optional:true, emit: duplicates
     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}"
diff --git a/modules/gffread/main.nf b/modules/gffread/main.nf
index e7893f8b..7c575c97 100644
--- a/modules/gffread/main.nf
+++ b/modules/gffread/main.nf
@@ -14,6 +14,9 @@ process GFFREAD {
     path "*.gtf"        , emit: gtf
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${gff.baseName}"
diff --git a/modules/glnexus/main.nf b/modules/glnexus/main.nf
index b8afca22..84da95a0 100644
--- a/modules/glnexus/main.nf
+++ b/modules/glnexus/main.nf
@@ -14,6 +14,9 @@ process GLNEXUS {
     tuple val(meta), path("*.bcf"), emit: bcf
     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}"
diff --git a/modules/graphmap2/align/main.nf b/modules/graphmap2/align/main.nf
index 554e585b..8834cc0a 100644
--- a/modules/graphmap2/align/main.nf
+++ b/modules/graphmap2/align/main.nf
@@ -17,6 +17,9 @@ process GRAPHMAP2_ALIGN {
     tuple val(meta), path("*.sam"), emit: sam
     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}"
diff --git a/modules/graphmap2/index/main.nf b/modules/graphmap2/index/main.nf
index fffc7bcb..ef240b6c 100644
--- a/modules/graphmap2/index/main.nf
+++ b/modules/graphmap2/index/main.nf
@@ -13,6 +13,9 @@ process GRAPHMAP2_INDEX {
     path "*.gmidx"      , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/gstama/collapse/main.nf b/modules/gstama/collapse/main.nf
index 1c06692d..36d8a311 100644
--- a/modules/gstama/collapse/main.nf
+++ b/modules/gstama/collapse/main.nf
@@ -24,6 +24,9 @@ process GSTAMA_COLLAPSE {
     tuple val(meta), path("*_varcov.txt")             , emit: varcov  , optional: true
     tuple val(meta), path("*_variants.txt")           , emit: variants, optional: true
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/gstama/merge/main.nf b/modules/gstama/merge/main.nf
index 53ff93e4..221ec3c9 100644
--- a/modules/gstama/merge/main.nf
+++ b/modules/gstama/merge/main.nf
@@ -18,6 +18,9 @@ process GSTAMA_MERGE {
     tuple val(meta), path("*_trans_report.txt"), emit: trans_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 ?: "${meta.id}"
diff --git a/modules/gtdbtk/classifywf/main.nf b/modules/gtdbtk/classifywf/main.nf
index 009efa8d..bf83c2ad 100644
--- a/modules/gtdbtk/classifywf/main.nf
+++ b/modules/gtdbtk/classifywf/main.nf
@@ -25,6 +25,9 @@ process GTDBTK_CLASSIFYWF {
     path "gtdbtk.${meta.assembler}-${meta.id}.failed_genomes.tsv"   , emit: failed
     path "versions.yml"                                             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
diff --git a/modules/gubbins/main.nf b/modules/gubbins/main.nf
index b4c6dc23..17a271d8 100644
--- a/modules/gubbins/main.nf
+++ b/modules/gubbins/main.nf
@@ -21,6 +21,9 @@ process GUBBINS {
     path "*.node_labelled.final_tree.tre"   , emit: tree_labelled
     path "versions.yml"                     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/gunc/downloaddb/main.nf b/modules/gunc/downloaddb/main.nf
index 430b862b..00638693 100644
--- a/modules/gunc/downloaddb/main.nf
+++ b/modules/gunc/downloaddb/main.nf
@@ -14,6 +14,9 @@ process GUNC_DOWNLOADDB {
     path "*.dmnd"       , emit: db
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/gunc/run/main.nf b/modules/gunc/run/main.nf
index 8508c9f0..ce9bd7c6 100644
--- a/modules/gunc/run/main.nf
+++ b/modules/gunc/run/main.nf
@@ -16,6 +16,9 @@ process GUNC_RUN {
     tuple val(meta), path("*all_levels.tsv")    , optional: true, emit: all_levels_tsv
     path "versions.yml"                                         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf
index 77a4e546..9d4b0666 100644
--- a/modules/gunzip/main.nf
+++ b/modules/gunzip/main.nf
@@ -14,6 +14,9 @@ process GUNZIP {
     tuple val(meta), path("$gunzip"), emit: gunzip
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     gunzip = archive.toString() - '.gz'
diff --git a/modules/hicap/main.nf b/modules/hicap/main.nf
index a96343f6..51fe0b83 100644
--- a/modules/hicap/main.nf
+++ b/modules/hicap/main.nf
@@ -18,6 +18,9 @@ process HICAP {
     tuple val(meta), path("*.tsv"), emit: tsv, 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}"
diff --git a/modules/hifiasm/main.nf b/modules/hifiasm/main.nf
index 208554d6..ea7c4976 100644
--- a/modules/hifiasm/main.nf
+++ b/modules/hifiasm/main.nf
@@ -25,6 +25,9 @@ process HIFIASM {
     tuple val(meta), path("*.hap2.p_ctg.gfa")  , emit: maternal_contigs , 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}"
diff --git a/modules/hisat2/align/main.nf b/modules/hisat2/align/main.nf
index ae888616..7f680018 100644
--- a/modules/hisat2/align/main.nf
+++ b/modules/hisat2/align/main.nf
@@ -20,6 +20,9 @@ process HISAT2_ALIGN {
     tuple val(meta), path("*fastq.gz"), optional:true, 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}"
diff --git a/modules/hisat2/build/main.nf b/modules/hisat2/build/main.nf
index 4e8cd02b..50f65e3a 100644
--- a/modules/hisat2/build/main.nf
+++ b/modules/hisat2/build/main.nf
@@ -19,6 +19,9 @@ process HISAT2_BUILD {
     path "hisat2"       , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 0
diff --git a/modules/hisat2/extractsplicesites/main.nf b/modules/hisat2/extractsplicesites/main.nf
index 302c35f1..94135977 100644
--- a/modules/hisat2/extractsplicesites/main.nf
+++ b/modules/hisat2/extractsplicesites/main.nf
@@ -16,6 +16,9 @@ process HISAT2_EXTRACTSPLICESITES {
     path "*.splice_sites.txt", emit: txt
     path "versions.yml"      , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/hmmcopy/gccounter/main.nf b/modules/hmmcopy/gccounter/main.nf
index a1de8b97..3911df6b 100644
--- a/modules/hmmcopy/gccounter/main.nf
+++ b/modules/hmmcopy/gccounter/main.nf
@@ -15,6 +15,9 @@ process HMMCOPY_GCCOUNTER {
     path "*.gc.wig"    , emit: wig
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/hmmcopy/generatemap/main.nf b/modules/hmmcopy/generatemap/main.nf
index 1d248853..c6c08725 100644
--- a/modules/hmmcopy/generatemap/main.nf
+++ b/modules/hmmcopy/generatemap/main.nf
@@ -16,6 +16,9 @@ process HMMCOPY_GENERATEMAP {
     path "*.map.bw"              , emit: bigwig
     path "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
 
diff --git a/modules/hmmcopy/mapcounter/main.nf b/modules/hmmcopy/mapcounter/main.nf
index ab20868e..b369d12b 100644
--- a/modules/hmmcopy/mapcounter/main.nf
+++ b/modules/hmmcopy/mapcounter/main.nf
@@ -15,6 +15,9 @@ process HMMCOPY_MAPCOUNTER {
     path "*.map.wig"              , emit: wig
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
 
diff --git a/modules/hmmcopy/readcounter/main.nf b/modules/hmmcopy/readcounter/main.nf
index a6e89f91..ff13770d 100644
--- a/modules/hmmcopy/readcounter/main.nf
+++ b/modules/hmmcopy/readcounter/main.nf
@@ -16,6 +16,9 @@ process HMMCOPY_READCOUNTER {
     tuple val(meta), path("*.wig"), emit: wig
     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}"
diff --git a/modules/hmmer/hmmalign/main.nf b/modules/hmmer/hmmalign/main.nf
index e6d04044..d3df3c89 100644
--- a/modules/hmmer/hmmalign/main.nf
+++ b/modules/hmmer/hmmalign/main.nf
@@ -15,6 +15,9 @@ process HMMER_HMMALIGN {
     tuple val(meta), path("*.sthlm.gz"), emit: sthlm
     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}"
diff --git a/modules/homer/annotatepeaks/main.nf b/modules/homer/annotatepeaks/main.nf
index 84e0241a..c9da82ed 100644
--- a/modules/homer/annotatepeaks/main.nf
+++ b/modules/homer/annotatepeaks/main.nf
@@ -18,6 +18,9 @@ process HOMER_ANNOTATEPEAKS {
     tuple val(meta), path("*annotatePeaks.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}"
diff --git a/modules/homer/findpeaks/main.nf b/modules/homer/findpeaks/main.nf
index 66de06b6..b9947774 100644
--- a/modules/homer/findpeaks/main.nf
+++ b/modules/homer/findpeaks/main.nf
@@ -16,6 +16,9 @@ process HOMER_FINDPEAKS {
     tuple val(meta), path("*peaks.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}"
diff --git a/modules/homer/maketagdirectory/main.nf b/modules/homer/maketagdirectory/main.nf
index 72e2091f..262998d5 100644
--- a/modules/homer/maketagdirectory/main.nf
+++ b/modules/homer/maketagdirectory/main.nf
@@ -17,6 +17,9 @@ process HOMER_MAKETAGDIRECTORY {
     tuple val(meta), path("tag_dir"), emit: tagdir
     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}"
diff --git a/modules/homer/makeucscfile/main.nf b/modules/homer/makeucscfile/main.nf
index 17e86947..c82435ea 100644
--- a/modules/homer/makeucscfile/main.nf
+++ b/modules/homer/makeucscfile/main.nf
@@ -16,6 +16,9 @@ process HOMER_MAKEUCSCFILE {
     tuple val(meta), path("tag_dir/*ucsc.bedGraph.gz"), emit: bedGraph
     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}"
diff --git a/modules/idr/main.nf b/modules/idr/main.nf
index 7e377878..d18ef2eb 100644
--- a/modules/idr/main.nf
+++ b/modules/idr/main.nf
@@ -18,6 +18,9 @@ process IDR {
     path "*.png"         , emit: png
     path "versions.yml"  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     if (peaks.toList().size < 2) {
diff --git a/modules/imputeme/vcftoprs/main.nf b/modules/imputeme/vcftoprs/main.nf
index 5fee90c2..8ce3f73d 100644
--- a/modules/imputeme/vcftoprs/main.nf
+++ b/modules/imputeme/vcftoprs/main.nf
@@ -14,6 +14,9 @@ process IMPUTEME_VCFTOPRS {
     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}"
diff --git a/modules/iqtree/main.nf b/modules/iqtree/main.nf
index 54a6486d..db394bd2 100644
--- a/modules/iqtree/main.nf
+++ b/modules/iqtree/main.nf
@@ -15,6 +15,9 @@ process IQTREE {
     path "*.treefile",    emit: phylogeny
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
diff --git a/modules/ismapper/main.nf b/modules/ismapper/main.nf
index a51cc01e..a2c79115 100644
--- a/modules/ismapper/main.nf
+++ b/modules/ismapper/main.nf
@@ -14,6 +14,9 @@ process ISMAPPER {
     tuple val(meta), path("results/*"), 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}"
diff --git a/modules/isoseq3/cluster/main.nf b/modules/isoseq3/cluster/main.nf
index fdd47971..fe1b10d4 100644
--- a/modules/isoseq3/cluster/main.nf
+++ b/modules/isoseq3/cluster/main.nf
@@ -24,6 +24,9 @@ process ISOSEQ3_CLUSTER {
     tuple val(meta), path("*.transcripts.singletons.bam.pbi"), optional: true, emit: singletons_pbi
     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}"
diff --git a/modules/isoseq3/refine/main.nf b/modules/isoseq3/refine/main.nf
index 5044cba2..25014811 100644
--- a/modules/isoseq3/refine/main.nf
+++ b/modules/isoseq3/refine/main.nf
@@ -19,6 +19,9 @@ process ISOSEQ3_REFINE {
     tuple val(meta), path("*.report.csv")          , 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}"
diff --git a/modules/ivar/consensus/main.nf b/modules/ivar/consensus/main.nf
index 96d00ce2..db6301e9 100644
--- a/modules/ivar/consensus/main.nf
+++ b/modules/ivar/consensus/main.nf
@@ -18,6 +18,9 @@ process IVAR_CONSENSUS {
     tuple val(meta), path("*.mpileup") , optional:true, emit: mpileup
     path "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/ivar/trim/main.nf b/modules/ivar/trim/main.nf
index 4d0c70a2..819aa5dd 100644
--- a/modules/ivar/trim/main.nf
+++ b/modules/ivar/trim/main.nf
@@ -16,6 +16,9 @@ process IVAR_TRIM {
     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}"
diff --git a/modules/ivar/variants/main.nf b/modules/ivar/variants/main.nf
index bb6e402b..85c4cacd 100644
--- a/modules/ivar/variants/main.nf
+++ b/modules/ivar/variants/main.nf
@@ -18,6 +18,9 @@ process IVAR_VARIANTS {
     tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
     path "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/jupyternotebook/main.nf b/modules/jupyternotebook/main.nf
index 871d6ccd..baed502c 100644
--- a/modules/jupyternotebook/main.nf
+++ b/modules/jupyternotebook/main.nf
@@ -22,6 +22,9 @@ process JUPYTERNOTEBOOK {
     tuple val(meta), path("artifacts/"), emit: artifacts, 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}"
diff --git a/modules/kallisto/index/main.nf b/modules/kallisto/index/main.nf
index 4dc9c6d0..0f10e564 100644
--- a/modules/kallisto/index/main.nf
+++ b/modules/kallisto/index/main.nf
@@ -14,6 +14,9 @@ process KALLISTO_INDEX {
     path "kallisto" , emit: idx
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/kallistobustools/count/main.nf b/modules/kallistobustools/count/main.nf
index d67eba31..d674aece 100644
--- a/modules/kallistobustools/count/main.nf
+++ b/modules/kallistobustools/count/main.nf
@@ -20,6 +20,9 @@ process KALLISTOBUSTOOLS_COUNT {
     tuple val(meta), path ("*.count"), emit: count
     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}"
diff --git a/modules/kallistobustools/ref/main.nf b/modules/kallistobustools/ref/main.nf
index 1e496f67..1e789615 100644
--- a/modules/kallistobustools/ref/main.nf
+++ b/modules/kallistobustools/ref/main.nf
@@ -21,6 +21,9 @@ process KALLISTOBUSTOOLS_REF {
     path "cdna_t2c.txt"   , optional:true, emit: cdna_t2c
     path "intron_t2c.txt" , optional:true, emit: intron_t2c
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     if (workflow_mode == "standard") {
diff --git a/modules/khmer/normalizebymedian/main.nf b/modules/khmer/normalizebymedian/main.nf
index 50b3d603..f89b2585 100644
--- a/modules/khmer/normalizebymedian/main.nf
+++ b/modules/khmer/normalizebymedian/main.nf
@@ -16,6 +16,9 @@ process KHMER_NORMALIZEBYMEDIAN {
     path "${name}.fastq.gz", emit: reads
     path "versions.yml"    , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     pe_args = pe_reads ? "--paired" : ""
diff --git a/modules/kleborate/main.nf b/modules/kleborate/main.nf
index 4a793793..88cbc951 100644
--- a/modules/kleborate/main.nf
+++ b/modules/kleborate/main.nf
@@ -14,6 +14,9 @@ process KLEBORATE {
     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}"
diff --git a/modules/kraken2/kraken2/main.nf b/modules/kraken2/kraken2/main.nf
index eaabb229..3ec5df52 100644
--- a/modules/kraken2/kraken2/main.nf
+++ b/modules/kraken2/kraken2/main.nf
@@ -17,6 +17,9 @@ process KRAKEN2_KRAKEN2 {
     tuple val(meta), path('*report.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}"
diff --git a/modules/krona/kronadb/main.nf b/modules/krona/kronadb/main.nf
index d8156035..afcb0694 100644
--- a/modules/krona/kronadb/main.nf
+++ b/modules/krona/kronadb/main.nf
@@ -12,6 +12,9 @@ process KRONA_KRONADB {
     path 'taxonomy/taxonomy.tab', emit: db
     path "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/krona/ktimporttaxonomy/main.nf b/modules/krona/ktimporttaxonomy/main.nf
index bc79c98c..7837bb87 100644
--- a/modules/krona/ktimporttaxonomy/main.nf
+++ b/modules/krona/ktimporttaxonomy/main.nf
@@ -17,6 +17,9 @@ process KRONA_KTIMPORTTAXONOMY {
     tuple val(meta), path ('*.html'), emit: html
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/last/dotplot/main.nf b/modules/last/dotplot/main.nf
index e8857403..a71d001a 100644
--- a/modules/last/dotplot/main.nf
+++ b/modules/last/dotplot/main.nf
@@ -16,6 +16,9 @@ process LAST_DOTPLOT {
     tuple val(meta), path("*.png"), optional:true, emit: png
     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}"
diff --git a/modules/last/lastal/main.nf b/modules/last/lastal/main.nf
index b5ac8bfe..882b16cd 100644
--- a/modules/last/lastal/main.nf
+++ b/modules/last/lastal/main.nf
@@ -15,6 +15,9 @@ process LAST_LASTAL {
     tuple val(meta), path("*.maf.gz"), emit: maf
     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}"
diff --git a/modules/last/lastdb/main.nf b/modules/last/lastdb/main.nf
index e9895c5c..0747ba4d 100644
--- a/modules/last/lastdb/main.nf
+++ b/modules/last/lastdb/main.nf
@@ -14,6 +14,9 @@ process LAST_LASTDB {
     tuple val(meta), path("lastdb"), emit: index
     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}"
diff --git a/modules/last/mafconvert/main.nf b/modules/last/mafconvert/main.nf
index ca60e7fe..8ffec2f9 100644
--- a/modules/last/mafconvert/main.nf
+++ b/modules/last/mafconvert/main.nf
@@ -23,6 +23,9 @@ process LAST_MAFCONVERT {
     tuple val(meta), path("*.tab.gz"),      optional:true, emit: tab_gz
     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}"
diff --git a/modules/last/mafswap/main.nf b/modules/last/mafswap/main.nf
index 0a58b027..55f6a1a9 100644
--- a/modules/last/mafswap/main.nf
+++ b/modules/last/mafswap/main.nf
@@ -14,6 +14,9 @@ process LAST_MAFSWAP {
     tuple val(meta), path("*.maf.gz"), emit: maf
     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}"
diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf
index ca981e1c..6bc64930 100644
--- a/modules/last/postmask/main.nf
+++ b/modules/last/postmask/main.nf
@@ -14,6 +14,9 @@ process LAST_POSTMASK {
     tuple val(meta), path("*.maf.gz"), emit: maf
     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}"
diff --git a/modules/last/split/main.nf b/modules/last/split/main.nf
index 60ed135b..433eff0c 100644
--- a/modules/last/split/main.nf
+++ b/modules/last/split/main.nf
@@ -14,6 +14,9 @@ process LAST_SPLIT {
     tuple val(meta), path("*.maf.gz"), emit: maf
     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}"
diff --git a/modules/last/train/main.nf b/modules/last/train/main.nf
index 471db7c1..23f4f36b 100644
--- a/modules/last/train/main.nf
+++ b/modules/last/train/main.nf
@@ -15,6 +15,9 @@ process LAST_TRAIN {
     tuple val(meta), path("*.par"), emit: param_file
     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}"
diff --git a/modules/leehom/main.nf b/modules/leehom/main.nf
index b5cb2dcb..906d094e 100644
--- a/modules/leehom/main.nf
+++ b/modules/leehom/main.nf
@@ -23,6 +23,9 @@ process LEEHOM {
     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}"
diff --git a/modules/lima/main.nf b/modules/lima/main.nf
index 691e43f2..e98fd157 100644
--- a/modules/lima/main.nf
+++ b/modules/lima/main.nf
@@ -28,6 +28,9 @@ process LIMA {
     tuple val(meta), path("*.clips")            , optional: true, emit: clips
     tuple val(meta), path("*.guess")            , optional: true, emit: guess
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/lissero/main.nf b/modules/lissero/main.nf
index 667697ef..29995db8 100644
--- a/modules/lissero/main.nf
+++ b/modules/lissero/main.nf
@@ -14,6 +14,9 @@ process LISSERO {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/lofreq/call/main.nf b/modules/lofreq/call/main.nf
index d7fd078b..773bc212 100644
--- a/modules/lofreq/call/main.nf
+++ b/modules/lofreq/call/main.nf
@@ -15,6 +15,9 @@ process LOFREQ_CALL {
     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}"
diff --git a/modules/lofreq/callparallel/main.nf b/modules/lofreq/callparallel/main.nf
index 764efcc5..4dffc302 100644
--- a/modules/lofreq/callparallel/main.nf
+++ b/modules/lofreq/callparallel/main.nf
@@ -16,6 +16,9 @@ process LOFREQ_CALLPARALLEL {
     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}"
diff --git a/modules/lofreq/filter/main.nf b/modules/lofreq/filter/main.nf
index 34a5aef8..bddc012f 100644
--- a/modules/lofreq/filter/main.nf
+++ b/modules/lofreq/filter/main.nf
@@ -14,6 +14,9 @@ process LOFREQ_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}"
diff --git a/modules/lofreq/indelqual/main.nf b/modules/lofreq/indelqual/main.nf
index 5e5b8f44..ac53d70f 100644
--- a/modules/lofreq/indelqual/main.nf
+++ b/modules/lofreq/indelqual/main.nf
@@ -15,6 +15,9 @@ process LOFREQ_INDELQUAL {
     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}"
diff --git a/modules/macrel/contigs/main.nf b/modules/macrel/contigs/main.nf
index 558ef6e8..65db4d3e 100644
--- a/modules/macrel/contigs/main.nf
+++ b/modules/macrel/contigs/main.nf
@@ -18,6 +18,9 @@ process MACREL_CONTIGS {
     tuple val(meta), path("*/*_log.txt")            , emit: log_file
     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}"
diff --git a/modules/macs2/callpeak/main.nf b/modules/macs2/callpeak/main.nf
index c5c88f8e..9aaf97a9 100644
--- a/modules/macs2/callpeak/main.nf
+++ b/modules/macs2/callpeak/main.nf
@@ -20,6 +20,9 @@ process MACS2_CALLPEAK {
     tuple val(meta), path("*.bed")       , optional:true, emit: bed
     tuple val(meta), path("*.bdg")       , optional:true, emit: bdg
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/malt/build/main.nf b/modules/malt/build/main.nf
index d1b0c427..8eeb304b 100644
--- a/modules/malt/build/main.nf
+++ b/modules/malt/build/main.nf
@@ -18,6 +18,9 @@ process MALT_BUILD {
     path "versions.yml"  , emit: versions
     path "malt-build.log", emit: log
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 6
diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf
index 5e81667e..99657305 100644
--- a/modules/malt/run/main.nf
+++ b/modules/malt/run/main.nf
@@ -17,6 +17,9 @@ process MALT_RUN {
     path "*.log"                           , emit: log
     path "versions.yml"                    , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 6
diff --git a/modules/maltextract/main.nf b/modules/maltextract/main.nf
index e3a42016..75710141 100644
--- a/modules/maltextract/main.nf
+++ b/modules/maltextract/main.nf
@@ -16,6 +16,9 @@ process MALTEXTRACT {
     path "results"      , emit: results
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/manta/germline/main.nf b/modules/manta/germline/main.nf
index 2a8c0acc..fab789ec 100644
--- a/modules/manta/germline/main.nf
+++ b/modules/manta/germline/main.nf
@@ -23,6 +23,9 @@ process MANTA_GERMLINE {
     tuple val(meta), path("*diploid_sv.vcf.gz.tbi")            , emit: diploid_sv_vcf_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}"
diff --git a/modules/manta/somatic/main.nf b/modules/manta/somatic/main.nf
index 1d62635b..886a8fb9 100644
--- a/modules/manta/somatic/main.nf
+++ b/modules/manta/somatic/main.nf
@@ -25,6 +25,9 @@ process MANTA_SOMATIC {
     tuple val(meta), path("*.somatic_sv.vcf.gz.tbi")             , emit: somatic_sv_vcf_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}"
diff --git a/modules/manta/tumoronly/main.nf b/modules/manta/tumoronly/main.nf
index 63f7a840..3d52b16e 100644
--- a/modules/manta/tumoronly/main.nf
+++ b/modules/manta/tumoronly/main.nf
@@ -23,6 +23,9 @@ process MANTA_TUMORONLY {
     tuple val(meta), path("*tumor_sv.vcf.gz.tbi")              , emit: tumor_sv_vcf_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}"
diff --git a/modules/mapdamage2/main.nf b/modules/mapdamage2/main.nf
index e3668fda..53007115 100644
--- a/modules/mapdamage2/main.nf
+++ b/modules/mapdamage2/main.nf
@@ -32,6 +32,9 @@ process MAPDAMAGE2 {
     tuple val(meta), path("*/"), optional: true                                           ,emit: folder
     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}"
diff --git a/modules/mash/dist/main.nf b/modules/mash/dist/main.nf
index 323bd339..270767b5 100644
--- a/modules/mash/dist/main.nf
+++ b/modules/mash/dist/main.nf
@@ -15,6 +15,9 @@ process MASH_DIST {
     tuple val(meta), path("*.txt"), emit: dist
     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}"
diff --git a/modules/mash/sketch/main.nf b/modules/mash/sketch/main.nf
index d93641f7..54263af7 100644
--- a/modules/mash/sketch/main.nf
+++ b/modules/mash/sketch/main.nf
@@ -14,6 +14,9 @@ process MASH_SKETCH {
     tuple val(meta), path("*.mash_stats") , 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}"
diff --git a/modules/mashtree/main.nf b/modules/mashtree/main.nf
index 5da2f805..4cd9af19 100644
--- a/modules/mashtree/main.nf
+++ b/modules/mashtree/main.nf
@@ -15,6 +15,9 @@ process MASHTREE {
     tuple val(meta), path("*.tsv"), emit: matrix
     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}"
diff --git a/modules/maxbin2/main.nf b/modules/maxbin2/main.nf
index 4d384391..7b818d00 100644
--- a/modules/maxbin2/main.nf
+++ b/modules/maxbin2/main.nf
@@ -21,6 +21,9 @@ process MAXBIN2 {
     tuple val(meta), path("*_gene.tar.gz"), emit: marker_genes, 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}"
diff --git a/modules/medaka/main.nf b/modules/medaka/main.nf
index 761b1c34..da77d0f0 100644
--- a/modules/medaka/main.nf
+++ b/modules/medaka/main.nf
@@ -14,6 +14,9 @@ process MEDAKA {
     tuple val(meta), path("*.fa.gz"), emit: assembly
     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}"
diff --git a/modules/megahit/main.nf b/modules/megahit/main.nf
index 7b511883..6e6a1ad1 100644
--- a/modules/megahit/main.nf
+++ b/modules/megahit/main.nf
@@ -18,6 +18,9 @@ process MEGAHIT {
     tuple val(meta), path("megahit_out/intermediate_contigs/k*.final.contigs.fa.gz"), emit: kfinal_contigs
     path "versions.yml"                                                             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/meningotype/main.nf b/modules/meningotype/main.nf
index c3b65b9d..24c30029 100644
--- a/modules/meningotype/main.nf
+++ b/modules/meningotype/main.nf
@@ -14,6 +14,9 @@ process MENINGOTYPE {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/metabat2/jgisummarizebamcontigdepths/main.nf
index 4a5869b6..7125eeb2 100644
--- a/modules/metabat2/jgisummarizebamcontigdepths/main.nf
+++ b/modules/metabat2/jgisummarizebamcontigdepths/main.nf
@@ -14,6 +14,9 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
     tuple val(meta), path("*.txt.gz"), emit: depth
     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}"
diff --git a/modules/metabat2/metabat2/main.nf b/modules/metabat2/metabat2/main.nf
index a8af0ae9..23ebe19a 100644
--- a/modules/metabat2/metabat2/main.nf
+++ b/modules/metabat2/metabat2/main.nf
@@ -18,6 +18,9 @@ process METABAT2_METABAT2 {
     tuple val(meta), path("bins/*.fa.gz")           , optional:true , 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}"
diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf
index 64965af3..3fc6b277 100644
--- a/modules/metaphlan3/main.nf
+++ b/modules/metaphlan3/main.nf
@@ -17,6 +17,9 @@ process METAPHLAN3 {
     tuple val(meta), path('*.bowtie2out.txt'), optional:true, emit: bt2out
     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}"
diff --git a/modules/methyldackel/extract/main.nf b/modules/methyldackel/extract/main.nf
index a39c0305..b4242073 100644
--- a/modules/methyldackel/extract/main.nf
+++ b/modules/methyldackel/extract/main.nf
@@ -16,6 +16,9 @@ process METHYLDACKEL_EXTRACT {
     tuple val(meta), path("*.bedGraph"), emit: bedgraph
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/methyldackel/mbias/main.nf b/modules/methyldackel/mbias/main.nf
index 021f76f1..755e62f8 100644
--- a/modules/methyldackel/mbias/main.nf
+++ b/modules/methyldackel/mbias/main.nf
@@ -16,6 +16,9 @@ process METHYLDACKEL_MBIAS {
     tuple val(meta), path("*.mbias.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}"
diff --git a/modules/minia/main.nf b/modules/minia/main.nf
index 968cafa5..87dd74f9 100644
--- a/modules/minia/main.nf
+++ b/modules/minia/main.nf
@@ -16,6 +16,9 @@ process MINIA {
     tuple val(meta), path('*.h5')        , emit: h5
     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}"
diff --git a/modules/miniasm/main.nf b/modules/miniasm/main.nf
index b0db6925..f77b10f2 100644
--- a/modules/miniasm/main.nf
+++ b/modules/miniasm/main.nf
@@ -15,6 +15,9 @@ process MINIASM {
     tuple val(meta), path("*.fasta.gz"), emit: assembly
     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}"
diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index 500250e9..fe06f14d 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -15,6 +15,9 @@ process MINIMAP2_ALIGN {
     tuple val(meta), path("*.paf"), emit: paf
     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}"
diff --git a/modules/minimap2/index/main.nf b/modules/minimap2/index/main.nf
index 10cdd142..3dfeb861 100644
--- a/modules/minimap2/index/main.nf
+++ b/modules/minimap2/index/main.nf
@@ -13,6 +13,9 @@ process MINIMAP2_INDEX {
     path "*.mmi"        , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/mlst/main.nf b/modules/mlst/main.nf
index b2983b82..65396548 100644
--- a/modules/mlst/main.nf
+++ b/modules/mlst/main.nf
@@ -14,6 +14,9 @@ process MLST {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf
index d2669b7e..cc7bc86b 100644
--- a/modules/mosdepth/main.nf
+++ b/modules/mosdepth/main.nf
@@ -22,6 +22,9 @@ process MOSDEPTH {
     tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_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 ?: "${meta.id}"
diff --git a/modules/msisensor/msi/main.nf b/modules/msisensor/msi/main.nf
index 398b34a6..954c5bec 100644
--- a/modules/msisensor/msi/main.nf
+++ b/modules/msisensor/msi/main.nf
@@ -17,6 +17,9 @@ process MSISENSOR_MSI {
     tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
     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}"
diff --git a/modules/msisensor/scan/main.nf b/modules/msisensor/scan/main.nf
index 223b4f44..399513ce 100644
--- a/modules/msisensor/scan/main.nf
+++ b/modules/msisensor/scan/main.nf
@@ -14,6 +14,9 @@ process MSISENSOR_SCAN {
     tuple val(meta), path("*.tab"), 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}"
diff --git a/modules/mtnucratio/main.nf b/modules/mtnucratio/main.nf
index 83d6ea2b..cb8d27e3 100644
--- a/modules/mtnucratio/main.nf
+++ b/modules/mtnucratio/main.nf
@@ -16,6 +16,9 @@ process MTNUCRATIO {
     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}"
diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf
index 3dceb162..0ff7cac1 100644
--- a/modules/multiqc/main.nf
+++ b/modules/multiqc/main.nf
@@ -15,6 +15,9 @@ process MULTIQC {
     path "*_plots"             , optional:true, emit: plots
     path "versions.yml"        , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/mummer/main.nf b/modules/mummer/main.nf
index 39ad3e8b..1fe91404 100644
--- a/modules/mummer/main.nf
+++ b/modules/mummer/main.nf
@@ -16,6 +16,9 @@ process MUMMER {
     tuple val(meta), path("*.coords"), emit: coords
     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}"
diff --git a/modules/muscle/main.nf b/modules/muscle/main.nf
index 6d549aaa..b2a1a131 100644
--- a/modules/muscle/main.nf
+++ b/modules/muscle/main.nf
@@ -21,6 +21,9 @@ process MUSCLE {
     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}"
diff --git a/modules/nanolyse/main.nf b/modules/nanolyse/main.nf
index 0ad0f799..2b4f0928 100644
--- a/modules/nanolyse/main.nf
+++ b/modules/nanolyse/main.nf
@@ -16,6 +16,9 @@ process NANOLYSE {
     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}"
diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf
index c3fb8a37..083e2374 100644
--- a/modules/nanoplot/main.nf
+++ b/modules/nanoplot/main.nf
@@ -17,6 +17,9 @@ process NANOPLOT {
     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 input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" :
diff --git a/modules/ncbigenomedownload/main.nf b/modules/ncbigenomedownload/main.nf
index 9897c861..60323dc8 100644
--- a/modules/ncbigenomedownload/main.nf
+++ b/modules/ncbigenomedownload/main.nf
@@ -27,6 +27,9 @@ process NCBIGENOMEDOWNLOAD {
     tuple val(meta), path("*_assembly_stats.txt")     , emit: stats   , 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 ?: "${meta.id}"
diff --git a/modules/nextclade/datasetget/main.nf b/modules/nextclade/datasetget/main.nf
index 75bb88f3..4dd82ee3 100644
--- a/modules/nextclade/datasetget/main.nf
+++ b/modules/nextclade/datasetget/main.nf
@@ -16,6 +16,9 @@ process NEXTCLADE_DATASETGET {
     path "$prefix"     , emit: dataset
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${dataset}"
diff --git a/modules/nextclade/run/main.nf b/modules/nextclade/run/main.nf
index b3d101ce..4d4bdb88 100644
--- a/modules/nextclade/run/main.nf
+++ b/modules/nextclade/run/main.nf
@@ -18,6 +18,9 @@ process NEXTCLADE_RUN {
     tuple val(meta), path("${prefix}.tree.json"), emit: json_tree
     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}"
diff --git a/modules/ngmaster/main.nf b/modules/ngmaster/main.nf
index 7d04031c..ef288e8f 100644
--- a/modules/ngmaster/main.nf
+++ b/modules/ngmaster/main.nf
@@ -14,6 +14,9 @@ process NGMASTER {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/nucmer/main.nf b/modules/nucmer/main.nf
index 4e296515..5b70abd9 100644
--- a/modules/nucmer/main.nf
+++ b/modules/nucmer/main.nf
@@ -15,6 +15,9 @@ process NUCMER {
     tuple val(meta), path("*.coords"), emit: coords
     path "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/optitype/main.nf b/modules/optitype/main.nf
index d27f7f9f..984d4669 100644
--- a/modules/optitype/main.nf
+++ b/modules/optitype/main.nf
@@ -14,6 +14,9 @@ process OPTITYPE {
     tuple val(meta), path("${prefix}"), emit: output
     path "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args  = task.ext.args   ?: ''
     def args2 = task.ext.args2  ?: ''
diff --git a/modules/pairix/main.nf b/modules/pairix/main.nf
index c1b9658c..0b8c63c6 100644
--- a/modules/pairix/main.nf
+++ b/modules/pairix/main.nf
@@ -14,6 +14,9 @@ process PAIRIX {
     tuple val(meta), path(pair), path("*.px2"), emit: index
     path "versions.yml"                       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/pairtools/dedup/main.nf b/modules/pairtools/dedup/main.nf
index fe59e155..2c171e7a 100644
--- a/modules/pairtools/dedup/main.nf
+++ b/modules/pairtools/dedup/main.nf
@@ -15,6 +15,9 @@ process PAIRTOOLS_DEDUP {
     tuple val(meta), path("*.pairs.stat"), emit: stat
     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}"
diff --git a/modules/pairtools/flip/main.nf b/modules/pairtools/flip/main.nf
index 376191ce..4959c4ee 100644
--- a/modules/pairtools/flip/main.nf
+++ b/modules/pairtools/flip/main.nf
@@ -15,6 +15,9 @@ process PAIRTOOLS_FLIP {
     tuple val(meta), path("*.flip.gz"), emit: flip
     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}"
diff --git a/modules/pairtools/parse/main.nf b/modules/pairtools/parse/main.nf
index 7bd778c9..190346b1 100644
--- a/modules/pairtools/parse/main.nf
+++ b/modules/pairtools/parse/main.nf
@@ -16,6 +16,9 @@ process PAIRTOOLS_PARSE {
     tuple val(meta), path("*.pairsam.stat"), emit: stat
     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}"
diff --git a/modules/pairtools/restrict/main.nf b/modules/pairtools/restrict/main.nf
index 8759f709..59e18648 100644
--- a/modules/pairtools/restrict/main.nf
+++ b/modules/pairtools/restrict/main.nf
@@ -15,6 +15,9 @@ process PAIRTOOLS_RESTRICT {
     tuple val(meta), path("*.pairs.gz"), emit: restrict
     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}"
diff --git a/modules/pairtools/select/main.nf b/modules/pairtools/select/main.nf
index a6d62ba7..9d434884 100644
--- a/modules/pairtools/select/main.nf
+++ b/modules/pairtools/select/main.nf
@@ -15,6 +15,9 @@ process PAIRTOOLS_SELECT {
     tuple val(meta), path("*.unselected.pairs.gz"), emit: unselected
     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}"
diff --git a/modules/pairtools/sort/main.nf b/modules/pairtools/sort/main.nf
index d5996dd0..15ed56d1 100644
--- a/modules/pairtools/sort/main.nf
+++ b/modules/pairtools/sort/main.nf
@@ -14,6 +14,9 @@ process PAIRTOOLS_SORT {
     tuple val(meta), path("*.pairs.gz"), 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}"
diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf
index 6c8682e3..9fbc69b8 100644
--- a/modules/pangolin/main.nf
+++ b/modules/pangolin/main.nf
@@ -14,6 +14,9 @@ process PANGOLIN {
     tuple val(meta), path('*.csv'), 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}"
diff --git a/modules/paraclu/main.nf b/modules/paraclu/main.nf
index cc16674e..1dcc4f90 100644
--- a/modules/paraclu/main.nf
+++ b/modules/paraclu/main.nf
@@ -17,6 +17,9 @@ process PARACLU {
     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}"
diff --git a/modules/pbbam/pbmerge/main.nf b/modules/pbbam/pbmerge/main.nf
index e0525cb1..aa0ca788 100644
--- a/modules/pbbam/pbmerge/main.nf
+++ b/modules/pbbam/pbmerge/main.nf
@@ -15,6 +15,9 @@ process PBBAM_PBMERGE {
     tuple val(meta), path("*.pbi"), emit: pbi
     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}"
diff --git a/modules/pbccs/main.nf b/modules/pbccs/main.nf
index 440fbc72..5bfae1bf 100644
--- a/modules/pbccs/main.nf
+++ b/modules/pbccs/main.nf
@@ -20,6 +20,9 @@ process PBCCS {
     tuple val(meta), path("*.metrics.json.gz"), 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}"
diff --git a/modules/peddy/main.nf b/modules/peddy/main.nf
index 1aa02a4f..50cdc698 100644
--- a/modules/peddy/main.nf
+++ b/modules/peddy/main.nf
@@ -18,6 +18,9 @@ process PEDDY {
     tuple val(meta), path("*.png")      , optional: true, emit: png
     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}"
diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf
index 6fe34cc2..c8325b05 100644
--- a/modules/phantompeakqualtools/main.nf
+++ b/modules/phantompeakqualtools/main.nf
@@ -18,6 +18,9 @@ process PHANTOMPEAKQUALTOOLS {
     tuple val(meta), path("*.Rdata"), emit: rdata
     path  "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/phyloflash/main.nf b/modules/phyloflash/main.nf
index 9ebc40de..23c38d56 100644
--- a/modules/phyloflash/main.nf
+++ b/modules/phyloflash/main.nf
@@ -16,6 +16,9 @@ process PHYLOFLASH {
     tuple val(meta), path("${meta.id}*/*"), 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}"
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index ae3e4d96..07e8504f 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -18,6 +18,9 @@ process PICARD_COLLECTHSMETRICS {
     tuple val(meta), path("*collecthsmetrics.txt"), emit: hs_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}"
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index 9511f7a4..e023ea3c 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -16,6 +16,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tuple val(meta), path("*.pdf")    , emit: pdf
     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}"
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index dd9da1b6..f4efaa4c 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -15,6 +15,9 @@ process PICARD_COLLECTWGSMETRICS {
     tuple val(meta), path("*_metrics"), 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}"
diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf
index 6a9c9c72..ab75abfa 100644
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@@ -15,6 +15,9 @@ process PICARD_FILTERSAMREADS {
     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}"
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index 7990d7e6..5196b6ed 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -16,6 +16,9 @@ process PICARD_MARKDUPLICATES {
     tuple val(meta), path("*.metrics.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}"
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index 96616a44..ef5c3980 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -14,6 +14,9 @@ process PICARD_MERGESAMFILES {
     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}"
diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf
index 6676eed6..adec17cb 100644
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@@ -15,6 +15,9 @@ process PICARD_SORTSAM {
     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}"
diff --git a/modules/pirate/main.nf b/modules/pirate/main.nf
index c7d7476c..20544a1b 100644
--- a/modules/pirate/main.nf
+++ b/modules/pirate/main.nf
@@ -15,6 +15,9 @@ process PIRATE {
     tuple val(meta), path("results/core_alignment.fasta"), optional: true, emit: aln
     path "versions.yml"                                                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/plasmidid/main.nf b/modules/plasmidid/main.nf
index 7404a678..7911d806 100644
--- a/modules/plasmidid/main.nf
+++ b/modules/plasmidid/main.nf
@@ -22,6 +22,9 @@ process PLASMIDID {
     tuple val(meta), path("${prefix}/kmer/")              , emit: kmer
     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}"
diff --git a/modules/plink/extract/main.nf b/modules/plink/extract/main.nf
index 688ada67..fa22b527 100644
--- a/modules/plink/extract/main.nf
+++ b/modules/plink/extract/main.nf
@@ -16,6 +16,9 @@ process PLINK_EXTRACT {
     tuple val(meta), path("*.fam"), emit: fam
     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}"
diff --git a/modules/plink/vcf/main.nf b/modules/plink/vcf/main.nf
index 719e90d2..0a69a021 100644
--- a/modules/plink/vcf/main.nf
+++ b/modules/plink/vcf/main.nf
@@ -17,6 +17,9 @@ process PLINK_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}"
diff --git a/modules/plink2/extract/main.nf b/modules/plink2/extract/main.nf
index 7eb24abc..89cffdc3 100644
--- a/modules/plink2/extract/main.nf
+++ b/modules/plink2/extract/main.nf
@@ -16,6 +16,9 @@ process PLINK2_EXTRACT {
     tuple val(meta), path("*.pvar.zst"), emit: extract_pvar
     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}"
diff --git a/modules/plink2/vcf/main.nf b/modules/plink2/vcf/main.nf
index 078ece1e..041cb4b9 100644
--- a/modules/plink2/vcf/main.nf
+++ b/modules/plink2/vcf/main.nf
@@ -16,6 +16,9 @@ process PLINK2_VCF {
     tuple val(meta), path("*.pvar"), emit: pvar
     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}"
diff --git a/modules/pmdtools/filter/main.nf b/modules/pmdtools/filter/main.nf
index b647b6d3..2d9d6eb3 100644
--- a/modules/pmdtools/filter/main.nf
+++ b/modules/pmdtools/filter/main.nf
@@ -16,6 +16,9 @@ process PMDTOOLS_FILTER {
     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 ?: ''
diff --git a/modules/porechop/main.nf b/modules/porechop/main.nf
index f5ad93f8..65982b8b 100644
--- a/modules/porechop/main.nf
+++ b/modules/porechop/main.nf
@@ -14,6 +14,9 @@ process PORECHOP {
     tuple val(meta), path("*.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}"
diff --git a/modules/preseq/lcextrap/main.nf b/modules/preseq/lcextrap/main.nf
index b5bd0620..d6dd19e2 100644
--- a/modules/preseq/lcextrap/main.nf
+++ b/modules/preseq/lcextrap/main.nf
@@ -16,6 +16,9 @@ process PRESEQ_LCEXTRAP {
     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 ?: "${meta.id}"
diff --git a/modules/prodigal/main.nf b/modules/prodigal/main.nf
index 63248931..5768952b 100644
--- a/modules/prodigal/main.nf
+++ b/modules/prodigal/main.nf
@@ -18,6 +18,9 @@ process PRODIGAL {
     tuple val(meta), path("${prefix}_all.txt"),             emit: all_gene_annotations
     path "versions.yml",                                    emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/prokka/main.nf b/modules/prokka/main.nf
index 551a17b9..3e46d1a1 100644
--- a/modules/prokka/main.nf
+++ b/modules/prokka/main.nf
@@ -27,6 +27,9 @@ process PROKKA {
     tuple val(meta), path("${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}"
diff --git a/modules/pycoqc/main.nf b/modules/pycoqc/main.nf
index e966b31c..a5e6fcb2 100644
--- a/modules/pycoqc/main.nf
+++ b/modules/pycoqc/main.nf
@@ -15,6 +15,9 @@ process PYCOQC {
     path "*.json"        , emit: json
     path  "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/pydamage/analyze/main.nf b/modules/pydamage/analyze/main.nf
index c06c592c..39e01fa1 100644
--- a/modules/pydamage/analyze/main.nf
+++ b/modules/pydamage/analyze/main.nf
@@ -14,6 +14,9 @@ process PYDAMAGE_ANALYZE {
     tuple val(meta), path("pydamage_results/pydamage_results.csv"), emit: 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}"
diff --git a/modules/pydamage/filter/main.nf b/modules/pydamage/filter/main.nf
index ab0b2115..a748875a 100644
--- a/modules/pydamage/filter/main.nf
+++ b/modules/pydamage/filter/main.nf
@@ -14,6 +14,9 @@ process PYDAMAGE_FILTER {
     tuple val(meta), path("pydamage_results/pydamage_filtered_results.csv"), emit: 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}"
diff --git a/modules/qcat/main.nf b/modules/qcat/main.nf
index 7d81952d..4c75b003 100644
--- a/modules/qcat/main.nf
+++ b/modules/qcat/main.nf
@@ -15,6 +15,9 @@ process QCAT {
     tuple val(meta), path("fastq/*.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 ?: "${meta.id}"
diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf
index 973fd6a4..4bff0254 100644
--- a/modules/qualimap/bamqc/main.nf
+++ b/modules/qualimap/bamqc/main.nf
@@ -16,6 +16,9 @@ process QUALIMAP_BAMQC {
     tuple val(meta), path("${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 ?: "${meta.id}"
diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf
index d83fcd99..3b2f88ad 100644
--- a/modules/qualimap/rnaseq/main.nf
+++ b/modules/qualimap/rnaseq/main.nf
@@ -15,6 +15,9 @@ process QUALIMAP_RNASEQ {
     tuple val(meta), path("${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}"
diff --git a/modules/quast/main.nf b/modules/quast/main.nf
index e88051b5..beb797d4 100644
--- a/modules/quast/main.nf
+++ b/modules/quast/main.nf
@@ -18,6 +18,9 @@ process QUAST {
     path '*.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 ?: 'quast'
diff --git a/modules/racon/main.nf b/modules/racon/main.nf
index 9be5ce63..6f844896 100644
--- a/modules/racon/main.nf
+++ b/modules/racon/main.nf
@@ -14,6 +14,9 @@ process RACON {
     tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
     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}"
diff --git a/modules/rapidnj/main.nf b/modules/rapidnj/main.nf
index 04a08227..952bae4c 100644
--- a/modules/rapidnj/main.nf
+++ b/modules/rapidnj/main.nf
@@ -16,6 +16,9 @@ process RAPIDNJ {
     path "*.tre"       , emit: phylogeny
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/rasusa/main.nf b/modules/rasusa/main.nf
index c2893d18..47c8ece6 100644
--- a/modules/rasusa/main.nf
+++ b/modules/rasusa/main.nf
@@ -15,6 +15,9 @@ process RASUSA {
     tuple val(meta), path('*.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}"
diff --git a/modules/raven/main.nf b/modules/raven/main.nf
index 0d81b94b..8bcf6bb1 100644
--- a/modules/raven/main.nf
+++ b/modules/raven/main.nf
@@ -15,6 +15,9 @@ process RAVEN {
     tuple val(meta), path("*.gfa.gz")  , emit: gfa
     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}"
diff --git a/modules/raxmlng/main.nf b/modules/raxmlng/main.nf
index 62b6c78a..e872a4e6 100644
--- a/modules/raxmlng/main.nf
+++ b/modules/raxmlng/main.nf
@@ -14,6 +14,9 @@ process RAXMLNG {
     path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped
     path "versions.yml"    , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/rmarkdownnotebook/main.nf b/modules/rmarkdownnotebook/main.nf
index 18d8e150..336b0af0 100644
--- a/modules/rmarkdownnotebook/main.nf
+++ b/modules/rmarkdownnotebook/main.nf
@@ -23,6 +23,9 @@ process RMARKDOWNNOTEBOOK {
     tuple val(meta), path ("session_info.log"), emit: session_info
     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}"
diff --git a/modules/roary/main.nf b/modules/roary/main.nf
index edda3281..fabb3234 100644
--- a/modules/roary/main.nf
+++ b/modules/roary/main.nf
@@ -15,6 +15,9 @@ process ROARY {
     tuple val(meta), path("results/*.aln"), optional: true, emit: aln
     path "versions.yml"                                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf
index 4b2ada47..cf147a63 100644
--- a/modules/rsem/calculateexpression/main.nf
+++ b/modules/rsem/calculateexpression/main.nf
@@ -22,6 +22,9 @@ process RSEM_CALCULATEEXPRESSION {
     tuple val(meta), path("${prefix}.genome.bam")    , optional:true, emit: bam_genome
     tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf
index a5b8922a..2d2ca205 100644
--- a/modules/rsem/preparereference/main.nf
+++ b/modules/rsem/preparereference/main.nf
@@ -16,6 +16,9 @@ process RSEM_PREPAREREFERENCE {
     path "*transcripts.fa", emit: transcript_fasta
     path "versions.yml"   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/rseqc/bamstat/main.nf b/modules/rseqc/bamstat/main.nf
index 1141a13f..958221fd 100644
--- a/modules/rseqc/bamstat/main.nf
+++ b/modules/rseqc/bamstat/main.nf
@@ -14,6 +14,9 @@ process RSEQC_BAMSTAT {
     tuple val(meta), path("*.bam_stat.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}"
diff --git a/modules/rseqc/inferexperiment/main.nf b/modules/rseqc/inferexperiment/main.nf
index 2243c43e..23c1b688 100644
--- a/modules/rseqc/inferexperiment/main.nf
+++ b/modules/rseqc/inferexperiment/main.nf
@@ -15,6 +15,9 @@ process RSEQC_INFEREXPERIMENT {
     tuple val(meta), path("*.infer_experiment.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}"
diff --git a/modules/rseqc/innerdistance/main.nf b/modules/rseqc/innerdistance/main.nf
index 425737d6..b05661de 100644
--- a/modules/rseqc/innerdistance/main.nf
+++ b/modules/rseqc/innerdistance/main.nf
@@ -19,6 +19,9 @@ process RSEQC_INNERDISTANCE {
     tuple val(meta), path("*.r")          , optional:true, emit: rscript
     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}"
diff --git a/modules/rseqc/junctionannotation/main.nf b/modules/rseqc/junctionannotation/main.nf
index d2562e5c..c3401dc5 100644
--- a/modules/rseqc/junctionannotation/main.nf
+++ b/modules/rseqc/junctionannotation/main.nf
@@ -21,6 +21,9 @@ process RSEQC_JUNCTIONANNOTATION {
     tuple val(meta), path("*events.pdf")   , optional:true, emit: events_pdf
     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}"
diff --git a/modules/rseqc/junctionsaturation/main.nf b/modules/rseqc/junctionsaturation/main.nf
index 695762b5..11b62904 100644
--- a/modules/rseqc/junctionsaturation/main.nf
+++ b/modules/rseqc/junctionsaturation/main.nf
@@ -16,6 +16,9 @@ process RSEQC_JUNCTIONSATURATION {
     tuple val(meta), path("*.r")  , emit: rscript
     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}"
diff --git a/modules/rseqc/readdistribution/main.nf b/modules/rseqc/readdistribution/main.nf
index 333193e3..3198c5c6 100644
--- a/modules/rseqc/readdistribution/main.nf
+++ b/modules/rseqc/readdistribution/main.nf
@@ -15,6 +15,9 @@ process RSEQC_READDISTRIBUTION {
     tuple val(meta), path("*.read_distribution.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}"
diff --git a/modules/rseqc/readduplication/main.nf b/modules/rseqc/readduplication/main.nf
index 134f2e8d..cb989a5f 100644
--- a/modules/rseqc/readduplication/main.nf
+++ b/modules/rseqc/readduplication/main.nf
@@ -17,6 +17,9 @@ process RSEQC_READDUPLICATION {
     tuple val(meta), path("*.r")             , emit: rscript
     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}"
diff --git a/modules/rseqc/tin/main.nf b/modules/rseqc/tin/main.nf
index b7bff0f3..da58fc06 100644
--- a/modules/rseqc/tin/main.nf
+++ b/modules/rseqc/tin/main.nf
@@ -16,6 +16,9 @@ process RSEQC_TIN {
     tuple val(meta), path("*.xls"), emit: xls
     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}"
diff --git a/modules/salmon/index/main.nf b/modules/salmon/index/main.nf
index b0a2f973..737087f9 100644
--- a/modules/salmon/index/main.nf
+++ b/modules/salmon/index/main.nf
@@ -15,6 +15,9 @@ process SALMON_INDEX {
     path "salmon"       , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
diff --git a/modules/salmon/quant/main.nf b/modules/salmon/quant/main.nf
index 6cae4f72..bd4792c5 100644
--- a/modules/salmon/quant/main.nf
+++ b/modules/salmon/quant/main.nf
@@ -19,6 +19,9 @@ process SALMON_QUANT {
     tuple val(meta), path("${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}"
diff --git a/modules/samblaster/main.nf b/modules/samblaster/main.nf
index 4627b978..c881389a 100644
--- a/modules/samblaster/main.nf
+++ b/modules/samblaster/main.nf
@@ -14,6 +14,9 @@ process SAMBLASTER {
     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 ?: ''
diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf
index e553f218..69c2ff7b 100644
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@@ -19,6 +19,9 @@ process SAMTOOLS_AMPLICONCLIP {
     tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_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}"
diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf
index 32588dd7..4b78a46e 100644
--- a/modules/samtools/bam2fq/main.nf
+++ b/modules/samtools/bam2fq/main.nf
@@ -15,6 +15,9 @@ process SAMTOOLS_BAM2FQ {
     tuple val(meta), path("*.fq.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}"
diff --git a/modules/samtools/depth/main.nf b/modules/samtools/depth/main.nf
index 50b2ed5d..d68c5adf 100644
--- a/modules/samtools/depth/main.nf
+++ b/modules/samtools/depth/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_DEPTH {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf
index 58c445d8..b83a4952 100644
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_FAIDX {
     tuple val(meta), path ("*.fai"), emit: fai
     path "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf
index a2dae087..7eb60117 100644
--- a/modules/samtools/fastq/main.nf
+++ b/modules/samtools/fastq/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_FASTQ {
     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}"
diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf
index 89ac666d..c1a8164b 100644
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_FIXMATE {
     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}"
diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf
index 119adf77..c267922b 100644
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_FLAGSTAT {
     tuple val(meta), path("*.flagstat"), emit: flagstat
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf
index fc54e676..8a057413 100644
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_IDXSTATS {
     tuple val(meta), path("*.idxstats"), emit: idxstats
     path  "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf
index c4fa2c63..dfe0234f 100644
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@@ -16,6 +16,9 @@ process SAMTOOLS_INDEX {
     tuple val(meta), path("*.crai"), optional:true, emit: crai
     path  "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf
index a318bfc4..be6fe32e 100644
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@@ -16,6 +16,9 @@ process SAMTOOLS_MERGE {
     tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
     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}"
diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf
index c40f46d1..77afae60 100644
--- a/modules/samtools/mpileup/main.nf
+++ b/modules/samtools/mpileup/main.nf
@@ -15,6 +15,9 @@ process SAMTOOLS_MPILEUP {
     tuple val(meta), path("*.mpileup"), emit: mpileup
     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}"
diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf
index 42c7bbf4..0f2237cc 100644
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@@ -14,6 +14,9 @@ process SAMTOOLS_SORT {
     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}"
diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf
index 7209070d..f6fe3bfe 100644
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@@ -15,6 +15,9 @@ process SAMTOOLS_STATS {
     tuple val(meta), path("*.stats"), emit: stats
     path  "versions.yml"            , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def reference = fasta ? "--reference ${fasta}" : ""
diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index cb205d0b..aee21a4e 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -16,6 +16,9 @@ process SAMTOOLS_VIEW {
     tuple val(meta), path("*.cram"), emit: cram, 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 ?: ''
diff --git a/modules/scoary/main.nf b/modules/scoary/main.nf
index ca33041d..cfa58ab2 100644
--- a/modules/scoary/main.nf
+++ b/modules/scoary/main.nf
@@ -15,6 +15,9 @@ process SCOARY {
     tuple val(meta), path("*.csv"), emit: 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}"
diff --git a/modules/seacr/callpeak/main.nf b/modules/seacr/callpeak/main.nf
index 12b9205f..340c0eef 100644
--- a/modules/seacr/callpeak/main.nf
+++ b/modules/seacr/callpeak/main.nf
@@ -17,6 +17,9 @@ process SEACR_CALLPEAK {
     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}"
diff --git a/modules/seqkit/split2/main.nf b/modules/seqkit/split2/main.nf
index 5bed1dae..ff91d86b 100644
--- a/modules/seqkit/split2/main.nf
+++ b/modules/seqkit/split2/main.nf
@@ -14,6 +14,9 @@ process SEQKIT_SPLIT2 {
     tuple val(meta), path("**/*.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}"
diff --git a/modules/seqsero2/main.nf b/modules/seqsero2/main.nf
index 0a7aa6ad..a5393cf6 100644
--- a/modules/seqsero2/main.nf
+++ b/modules/seqsero2/main.nf
@@ -16,6 +16,9 @@ process SEQSERO2 {
     tuple val(meta), path("results/*_result.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}"
diff --git a/modules/seqtk/mergepe/main.nf b/modules/seqtk/mergepe/main.nf
index 299c9ea4..519a4ab9 100644
--- a/modules/seqtk/mergepe/main.nf
+++ b/modules/seqtk/mergepe/main.nf
@@ -14,6 +14,9 @@ process SEQTK_MERGEPE {
     tuple val(meta), path("*.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}"
diff --git a/modules/seqtk/sample/main.nf b/modules/seqtk/sample/main.nf
index 96e08fd4..a9a89370 100644
--- a/modules/seqtk/sample/main.nf
+++ b/modules/seqtk/sample/main.nf
@@ -15,6 +15,9 @@ process SEQTK_SAMPLE {
     tuple val(meta), path("*.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}"
diff --git a/modules/seqtk/subseq/main.nf b/modules/seqtk/subseq/main.nf
index abfe4faa..9dd58686 100644
--- a/modules/seqtk/subseq/main.nf
+++ b/modules/seqtk/subseq/main.nf
@@ -15,6 +15,9 @@ process SEQTK_SUBSEQ {
     path "*.gz"         , emit: sequences
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: ''
diff --git a/modules/sequenzautils/bam2seqz/main.nf b/modules/sequenzautils/bam2seqz/main.nf
index ce9d1962..f150e0bd 100644
--- a/modules/sequenzautils/bam2seqz/main.nf
+++ b/modules/sequenzautils/bam2seqz/main.nf
@@ -16,6 +16,9 @@ process SEQUENZAUTILS_BAM2SEQZ {
     tuple val(meta), path("*.gz"), emit: seqz
     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}"
diff --git a/modules/sequenzautils/gcwiggle/main.nf b/modules/sequenzautils/gcwiggle/main.nf
index a6fcb559..23cc75b6 100644
--- a/modules/sequenzautils/gcwiggle/main.nf
+++ b/modules/sequenzautils/gcwiggle/main.nf
@@ -14,6 +14,9 @@ process SEQUENZAUTILS_GCWIGGLE {
     tuple val(meta), path("*.wig.gz"), emit: wig
     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}"
diff --git a/modules/seqwish/induce/main.nf b/modules/seqwish/induce/main.nf
index 6d6b33e7..529629ac 100644
--- a/modules/seqwish/induce/main.nf
+++ b/modules/seqwish/induce/main.nf
@@ -17,6 +17,9 @@ process SEQWISH_INDUCE {
     tuple val(meta), path("*.gfa"), emit: gfa
     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}"
diff --git a/modules/shovill/main.nf b/modules/shovill/main.nf
index 1a56df27..20a4548f 100644
--- a/modules/shovill/main.nf
+++ b/modules/shovill/main.nf
@@ -18,6 +18,9 @@ process SHOVILL {
     tuple val(meta), path("contigs.{fastg,gfa,LastGraph}")      , optional:true, emit: gfa
     path "versions.yml"                                         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def memory = task.memory.toGiga()
diff --git a/modules/snpdists/main.nf b/modules/snpdists/main.nf
index c8d61161..29febc68 100644
--- a/modules/snpdists/main.nf
+++ b/modules/snpdists/main.nf
@@ -14,6 +14,9 @@ process SNPDISTS {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/snpeff/main.nf b/modules/snpeff/main.nf
index 6248fee3..1b4d5f43 100644
--- a/modules/snpeff/main.nf
+++ b/modules/snpeff/main.nf
@@ -17,6 +17,9 @@ process SNPEFF {
     path "*.csv"                      , emit: report
     path "versions.yml"               , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def avail_mem = 6
diff --git a/modules/snpsift/split/main.nf b/modules/snpsift/split/main.nf
index a83052ad..8531b4cb 100644
--- a/modules/snpsift/split/main.nf
+++ b/modules/snpsift/split/main.nf
@@ -14,6 +14,9 @@ process SNPSIFT_SPLIT {
     tuple val(meta), path("*.vcf"), emit: out_vcfs
     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}"
diff --git a/modules/snpsites/main.nf b/modules/snpsites/main.nf
index 60e694ac..33b1a2c9 100644
--- a/modules/snpsites/main.nf
+++ b/modules/snpsites/main.nf
@@ -15,6 +15,9 @@ process SNPSITES {
     path "versions.yml" , emit: versions
     env   CONSTANT_SITES, emit: constant_sites_string
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/sortmerna/main.nf b/modules/sortmerna/main.nf
index 5c0950d8..419d2914 100644
--- a/modules/sortmerna/main.nf
+++ b/modules/sortmerna/main.nf
@@ -16,6 +16,9 @@ process SORTMERNA {
     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}"
diff --git a/modules/spades/main.nf b/modules/spades/main.nf
index ba690d35..b7ece6f6 100644
--- a/modules/spades/main.nf
+++ b/modules/spades/main.nf
@@ -20,6 +20,9 @@ process SPADES {
     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}"
diff --git a/modules/spatyper/main.nf b/modules/spatyper/main.nf
index d04fd265..2a116f09 100644
--- a/modules/spatyper/main.nf
+++ b/modules/spatyper/main.nf
@@ -16,6 +16,9 @@ process SPATYPER {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/sratools/fasterqdump/main.nf b/modules/sratools/fasterqdump/main.nf
index 73e3673d..1980ffeb 100644
--- a/modules/sratools/fasterqdump/main.nf
+++ b/modules/sratools/fasterqdump/main.nf
@@ -14,6 +14,9 @@ process SRATOOLS_FASTERQDUMP {
     tuple val(meta), path(output), emit: reads
     path "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/sratools/prefetch/main.nf b/modules/sratools/prefetch/main.nf
index 1e1eb802..2233d0aa 100644
--- a/modules/sratools/prefetch/main.nf
+++ b/modules/sratools/prefetch/main.nf
@@ -15,6 +15,9 @@ process SRATOOLS_PREFETCH {
     tuple val(meta), path("$id"), emit: sra
     path "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
diff --git a/modules/staphopiasccmec/main.nf b/modules/staphopiasccmec/main.nf
index dbb61a27..dd173c2f 100644
--- a/modules/staphopiasccmec/main.nf
+++ b/modules/staphopiasccmec/main.nf
@@ -14,6 +14,9 @@ process STAPHOPIASCCMEC {
     tuple val(meta), path("*.tsv"), emit: tsv
     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}"
diff --git a/modules/star/align/main.nf b/modules/star/align/main.nf
index 9725496f..7c965d07 100644
--- a/modules/star/align/main.nf
+++ b/modules/star/align/main.nf
@@ -30,6 +30,9 @@ process STAR_ALIGN {
     tuple val(meta), path('*.tab')                   , optional:true, emit: tab
     tuple val(meta), path('*.out.junction')          , optional:true, emit: junction
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/star/genomegenerate/main.nf b/modules/star/genomegenerate/main.nf
index ad32c0dd..50d280dd 100644
--- a/modules/star/genomegenerate/main.nf
+++ b/modules/star/genomegenerate/main.nf
@@ -16,6 +16,9 @@ process STAR_GENOMEGENERATE {
     path "star"         , emit: index
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args_list = args.tokenize()
diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf
index 324be6df..1ce0da31 100644
--- a/modules/strelka/germline/main.nf
+++ b/modules/strelka/germline/main.nf
@@ -21,6 +21,9 @@ process STRELKA_GERMLINE {
     tuple val(meta), path("*genome.vcf.gz.tbi")  , emit: genome_vcf_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}"
diff --git a/modules/strelka/somatic/main.nf b/modules/strelka/somatic/main.nf
index a9766d01..22cce8cb 100644
--- a/modules/strelka/somatic/main.nf
+++ b/modules/strelka/somatic/main.nf
@@ -21,6 +21,9 @@ process STRELKA_SOMATIC {
     tuple val(meta), path("*.somatic_snvs.vcf.gz.tbi")  , emit: vcf_snvs_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}"
diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf
index 756dc6ec..aa11eb36 100644
--- a/modules/stringtie/merge/main.nf
+++ b/modules/stringtie/merge/main.nf
@@ -15,6 +15,9 @@ process STRINGTIE_MERGE {
     path "stringtie.merged.gtf", emit: gtf
     path  "versions.yml"       , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf
index 9d62a966..f37e347a 100644
--- a/modules/stringtie/stringtie/main.nf
+++ b/modules/stringtie/stringtie/main.nf
@@ -18,6 +18,9 @@ process STRINGTIE {
     tuple val(meta), path("*.ballgown")       , emit: ballgown
     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}"
diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf
index 53eb279e..18e2a92b 100644
--- a/modules/subread/featurecounts/main.nf
+++ b/modules/subread/featurecounts/main.nf
@@ -15,6 +15,9 @@ process SUBREAD_FEATURECOUNTS {
     tuple val(meta), path("*featureCounts.txt.summary"), emit: summary
     path "versions.yml"                                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf
new file mode 100644
index 00000000..1f479ea4
--- /dev/null
+++ b/modules/svdb/merge/main.nf
@@ -0,0 +1,52 @@
+process SVDB_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
+        'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
+
+    input:
+    tuple val(meta), path(vcfs)
+    val (priority)
+
+    output:
+    tuple val(meta), path("*_sv_merge.vcf"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input  = ""
+    for (int index = 0; index < vcfs.size(); index++) {
+        input += " ${vcfs[index]}:${priority[index]}"
+    }
+    """
+    svdb \\
+        --merge \\
+        $args \\
+        --priority ${priority.join(',')} \\
+        --vcf $input \\
+        > ${prefix}_sv_merge.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_sv_merge.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/svdb/merge/meta.yml b/modules/svdb/merge/meta.yml
new file mode 100644
index 00000000..2092ddd9
--- /dev/null
+++ b/modules/svdb/merge/meta.yml
@@ -0,0 +1,39 @@
+name: svdb_merge
+description: The merge module merges structural variants within one or more vcf files.
+keywords:
+  - structural variants
+tools:
+  - svdb:
+      description: structural variant database software
+      homepage: https://github.com/J35P312/SVDB
+      documentation: https://github.com/J35P312/SVDB/blob/master/README.md
+      licence: ['MIT']
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - priority:
+      type: list
+      description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator']
+  - vcfs:
+      type: list
+      description: Two or more VCF files. Order of files should correspond to the order of tags used for priority.
+      pattern: "*.{vcf,vcf.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: merged VCF file
+      pattern: "*_sv_merge.vcf"
+authors:
+  - "@ramprasadn"
diff --git a/modules/svdb/query/main.nf b/modules/svdb/query/main.nf
index 61f4c8e6..292fe4ce 100644
--- a/modules/svdb/query/main.nf
+++ b/modules/svdb/query/main.nf
@@ -15,6 +15,9 @@ process SVDB_QUERY {
     tuple val(meta), path("*_ann_svdbq.vcf"), 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}"
diff --git a/modules/tabix/bgzip/main.nf b/modules/tabix/bgzip/main.nf
index ed9362b2..90940a5d 100644
--- a/modules/tabix/bgzip/main.nf
+++ b/modules/tabix/bgzip/main.nf
@@ -14,6 +14,9 @@ process TABIX_BGZIP {
     tuple val(meta), path("*.gz"), emit: gz
     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}"
diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf
index e419d153..3f42ad21 100644
--- a/modules/tabix/bgziptabix/main.nf
+++ b/modules/tabix/bgziptabix/main.nf
@@ -14,6 +14,9 @@ process TABIX_BGZIPTABIX {
     tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi
     path  "versions.yml" ,                        emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf
index c721a554..5f516261 100644
--- a/modules/tabix/tabix/main.nf
+++ b/modules/tabix/tabix/main.nf
@@ -14,6 +14,9 @@ process TABIX_TABIX {
     tuple val(meta), path("*.tbi"), emit: tbi
     path  "versions.yml"          , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     """
diff --git a/modules/tbprofiler/profile/main.nf b/modules/tbprofiler/profile/main.nf
index 87175a39..17c94a34 100644
--- a/modules/tbprofiler/profile/main.nf
+++ b/modules/tbprofiler/profile/main.nf
@@ -18,6 +18,9 @@ process TBPROFILER_PROFILE {
     tuple val(meta), path("vcf/*.vcf.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}"
diff --git a/modules/tiddit/cov/main.nf b/modules/tiddit/cov/main.nf
index c5a1ca0f..a5f8c649 100644
--- a/modules/tiddit/cov/main.nf
+++ b/modules/tiddit/cov/main.nf
@@ -16,6 +16,9 @@ process TIDDIT_COV {
     tuple val(meta), path("*.wig"), optional: true, emit: wig
     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}"
diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index 08eecc01..454dfc54 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -18,6 +18,9 @@ process TIDDIT_SV {
     tuple val(meta), path("*.signals.tab"), emit: signals
     path  "versions.yml"                  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/transdecoder/longorf/main.nf b/modules/transdecoder/longorf/main.nf
index 214fd1f0..9d5c20f2 100644
--- a/modules/transdecoder/longorf/main.nf
+++ b/modules/transdecoder/longorf/main.nf
@@ -18,6 +18,9 @@ process TRANSDECODER_LONGORF {
     path("${meta.id}/")                       , emit: folder
     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}"
diff --git a/modules/transdecoder/predict/main.nf b/modules/transdecoder/predict/main.nf
index 97b24b3f..dccc031c 100644
--- a/modules/transdecoder/predict/main.nf
+++ b/modules/transdecoder/predict/main.nf
@@ -18,6 +18,9 @@ process TRANSDECODER_PREDICT {
     tuple val(meta), path("*.transdecoder.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}"
diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf
index ee40b780..9487c799 100644
--- a/modules/trimgalore/main.nf
+++ b/modules/trimgalore/main.nf
@@ -18,6 +18,9 @@ process TRIMGALORE {
     tuple val(meta), path("*.html"), emit: html optional true
     tuple val(meta), path("*.zip") , emit: zip optional true
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     // Calculate number of --cores for TrimGalore based on value of task.cpus
diff --git a/modules/ucsc/bed12tobigbed/main.nf b/modules/ucsc/bed12tobigbed/main.nf
index 742798b3..0c84cfe7 100644
--- a/modules/ucsc/bed12tobigbed/main.nf
+++ b/modules/ucsc/bed12tobigbed/main.nf
@@ -17,6 +17,9 @@ process UCSC_BED12TOBIGBED {
     tuple val(meta), path("*.bigBed"), emit: bigbed
     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}"
diff --git a/modules/ucsc/bedclip/main.nf b/modules/ucsc/bedclip/main.nf
index dacd7260..969a8f73 100755
--- a/modules/ucsc/bedclip/main.nf
+++ b/modules/ucsc/bedclip/main.nf
@@ -17,6 +17,9 @@ process UCSC_BEDCLIP {
     tuple val(meta), path("*.bedGraph"), emit: bedgraph
     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}"
diff --git a/modules/ucsc/bedgraphtobigwig/main.nf b/modules/ucsc/bedgraphtobigwig/main.nf
index 9ba306ab..ef0ca088 100644
--- a/modules/ucsc/bedgraphtobigwig/main.nf
+++ b/modules/ucsc/bedgraphtobigwig/main.nf
@@ -17,6 +17,9 @@ process UCSC_BEDGRAPHTOBIGWIG {
     tuple val(meta), path("*.bigWig"), emit: bigwig
     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}"
diff --git a/modules/ucsc/bigwigaverageoverbed/main.nf b/modules/ucsc/bigwigaverageoverbed/main.nf
index 1e97c83d..51d63de8 100644
--- a/modules/ucsc/bigwigaverageoverbed/main.nf
+++ b/modules/ucsc/bigwigaverageoverbed/main.nf
@@ -17,6 +17,9 @@ process UCSC_BIGWIGAVERAGEOVERBED {
     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}"
diff --git a/modules/ucsc/liftover/main.nf b/modules/ucsc/liftover/main.nf
index 3dd9531e..be8fad3e 100644
--- a/modules/ucsc/liftover/main.nf
+++ b/modules/ucsc/liftover/main.nf
@@ -18,6 +18,9 @@ process UCSC_LIFTOVER {
     tuple val(meta), path("*.unlifted.bed"), emit: unlifted
     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}"
diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf
index 6a1847b6..d07e7ec1 100644
--- a/modules/ucsc/wigtobigwig/main.nf
+++ b/modules/ucsc/wigtobigwig/main.nf
@@ -17,6 +17,9 @@ process UCSC_WIGTOBIGWIG {
     tuple val(meta), path("*.bw"), emit: bw
     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}"
diff --git a/modules/ultra/pipeline/main.nf b/modules/ultra/pipeline/main.nf
index f2dcb543..c86a5802 100644
--- a/modules/ultra/pipeline/main.nf
+++ b/modules/ultra/pipeline/main.nf
@@ -16,6 +16,9 @@ process ULTRA_PIPELINE {
     tuple val(meta), path("*.sam"), emit: sam
     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}"
diff --git a/modules/umitools/dedup/main.nf b/modules/umitools/dedup/main.nf
index ce21437d..1e46a612 100644
--- a/modules/umitools/dedup/main.nf
+++ b/modules/umitools/dedup/main.nf
@@ -14,6 +14,9 @@ process UMITOOLS_DEDUP {
     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}"
diff --git a/modules/umitools/extract/main.nf b/modules/umitools/extract/main.nf
index fba8f054..22a405b9 100644
--- a/modules/umitools/extract/main.nf
+++ b/modules/umitools/extract/main.nf
@@ -15,6 +15,9 @@ process UMITOOLS_EXTRACT {
     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}"
diff --git a/modules/unicycler/main.nf b/modules/unicycler/main.nf
index 1ccc72a9..4d3721b0 100644
--- a/modules/unicycler/main.nf
+++ b/modules/unicycler/main.nf
@@ -16,6 +16,9 @@ process UNICYCLER {
     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 ?: "${meta.id}"
diff --git a/modules/untar/main.nf b/modules/untar/main.nf
index 6d1996e7..01205e60 100644
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@@ -14,6 +14,9 @@ process UNTAR {
     path "$untar"      , emit: untar
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
diff --git a/modules/unzip/main.nf b/modules/unzip/main.nf
index 294ac0b0..1ce4b89b 100644
--- a/modules/unzip/main.nf
+++ b/modules/unzip/main.nf
@@ -14,6 +14,9 @@ process UNZIP {
     path "${archive.baseName}/", emit: unzipped_archive
     path "versions.yml"        , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
     if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
diff --git a/modules/variantbam/main.nf b/modules/variantbam/main.nf
index 11059a9a..3370ca8f 100644
--- a/modules/variantbam/main.nf
+++ b/modules/variantbam/main.nf
@@ -16,6 +16,9 @@ process VARIANTBAM {
     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}"
diff --git a/modules/vcfanno/main.nf b/modules/vcfanno/main.nf
index 421fc0fa..77275963 100644
--- a/modules/vcfanno/main.nf
+++ b/modules/vcfanno/main.nf
@@ -15,6 +15,9 @@ process VCFANNO {
     tuple val(meta), path("*.vcf"), 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}"
diff --git a/modules/vcflib/vcfuniq/main.nf b/modules/vcflib/vcfuniq/main.nf
index 37fc51bc..a01e8485 100644
--- a/modules/vcflib/vcfuniq/main.nf
+++ b/modules/vcflib/vcfuniq/main.nf
@@ -16,6 +16,9 @@ process VCFLIB_VCFUNIQ {
     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}"
diff --git a/modules/vcftools/main.nf b/modules/vcftools/main.nf
index fbe646ca..78b95fae 100644
--- a/modules/vcftools/main.nf
+++ b/modules/vcftools/main.nf
@@ -81,6 +81,9 @@ process VCFTOOLS {
     tuple val(meta), path("*.diff.switch")            , optional:true, emit: diff_switch_error
     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}"
diff --git a/modules/yara/index/main.nf b/modules/yara/index/main.nf
index 77122c78..0fa5f00b 100644
--- a/modules/yara/index/main.nf
+++ b/modules/yara/index/main.nf
@@ -14,6 +14,9 @@ process YARA_INDEX {
     path "yara"        , emit: index
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args = task.ext.args ?: ''
 
diff --git a/modules/yara/mapper/main.nf b/modules/yara/mapper/main.nf
index 4539033d..9c993ac7 100644
--- a/modules/yara/mapper/main.nf
+++ b/modules/yara/mapper/main.nf
@@ -15,6 +15,9 @@ process YARA_MAPPER {
     tuple val(meta), path("*.mapped.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}"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index d41cf137..7fe48e85 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1449,6 +1449,10 @@ subread/featurecounts:
   - modules/subread/featurecounts/**
   - tests/modules/subread/featurecounts/**
 
+svdb/merge:
+  - modules/svdb/merge/**
+  - tests/modules/svdb/merge/**
+
 svdb/query:
   - modules/svdb/query/**
   - tests/modules/svdb/query/**
diff --git a/tests/modules/svdb/merge/main.nf b/tests/modules/svdb/merge/main.nf
new file mode 100644
index 00000000..f417c3f7
--- /dev/null
+++ b/tests/modules/svdb/merge/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SVDB_MERGE } from '../../../../modules/svdb/merge/main.nf'
+
+workflow test_svdb_merge {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true) ]
+            ]
+    priority = [ 'tiddit', 'cnvnator']
+
+    SVDB_MERGE ( input, priority )
+}
diff --git a/tests/modules/svdb/merge/nextflow.config b/tests/modules/svdb/merge/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/svdb/merge/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/svdb/merge/test.yml b/tests/modules/svdb/merge/test.yml
new file mode 100644
index 00000000..8d16562f
--- /dev/null
+++ b/tests/modules/svdb/merge/test.yml
@@ -0,0 +1,7 @@
+- name: svdb merge
+  command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
+  tags:
+    - svdb
+    - svdb/merge
+  files:
+    - path: output/svdb/test_sv_merge.vcf