From 3c03544c693bc0bf6e07cd064ead03ef37eb5fcc Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 4 Feb 2022 09:42:17 +0100
Subject: [PATCH] Add when: block

---
 modules/abacas/main.nf                               | 3 +++
 modules/adapterremoval/main.nf                       | 3 +++
 modules/agrvate/main.nf                              | 3 +++
 modules/allelecounter/main.nf                        | 3 +++
 modules/amps/main.nf                                 | 3 +++
 modules/arriba/main.nf                               | 3 +++
 modules/artic/guppyplex/main.nf                      | 3 +++
 modules/artic/minion/main.nf                         | 3 +++
 modules/assemblyscan/main.nf                         | 3 +++
 modules/ataqv/ataqv/main.nf                          | 3 +++
 modules/bakta/main.nf                                | 3 +++
 modules/bamaligncleaner/main.nf                      | 3 +++
 modules/bamcmp/main.nf                               | 3 +++
 modules/bamtools/convert/main.nf                     | 3 +++
 modules/bamtools/split/main.nf                       | 3 +++
 modules/bamutil/trimbam/main.nf                      | 3 +++
 modules/bandage/image/main.nf                        | 3 +++
 modules/bbmap/align/main.nf                          | 3 +++
 modules/bbmap/bbduk/main.nf                          | 3 +++
 modules/bbmap/bbsplit/main.nf                        | 3 +++
 modules/bbmap/index/main.nf                          | 3 +++
 modules/bcftools/concat/main.nf                      | 3 +++
 modules/bcftools/consensus/main.nf                   | 3 +++
 modules/bcftools/filter/main.nf                      | 3 +++
 modules/bcftools/index/main.nf                       | 3 +++
 modules/bcftools/isec/main.nf                        | 3 +++
 modules/bcftools/merge/main.nf                       | 3 +++
 modules/bcftools/mpileup/main.nf                     | 3 +++
 modules/bcftools/norm/main.nf                        | 3 +++
 modules/bcftools/query/main.nf                       | 3 +++
 modules/bcftools/reheader/main.nf                    | 3 +++
 modules/bcftools/sort/main.nf                        | 3 +++
 modules/bcftools/stats/main.nf                       | 3 +++
 modules/bcftools/view/main.nf                        | 3 +++
 modules/bedtools/bamtobed/main.nf                    | 3 +++
 modules/bedtools/complement/main.nf                  | 3 +++
 modules/bedtools/genomecov/main.nf                   | 3 +++
 modules/bedtools/getfasta/main.nf                    | 3 +++
 modules/bedtools/intersect/main.nf                   | 3 +++
 modules/bedtools/makewindows/main.nf                 | 3 +++
 modules/bedtools/maskfasta/main.nf                   | 3 +++
 modules/bedtools/merge/main.nf                       | 3 +++
 modules/bedtools/slop/main.nf                        | 3 +++
 modules/bedtools/sort/main.nf                        | 3 +++
 modules/bedtools/subtract/main.nf                    | 3 +++
 modules/bismark/align/main.nf                        | 3 +++
 modules/bismark/deduplicate/main.nf                  | 3 +++
 modules/bismark/genomepreparation/main.nf            | 3 +++
 modules/bismark/methylationextractor/main.nf         | 3 +++
 modules/bismark/report/main.nf                       | 3 +++
 modules/bismark/summary/main.nf                      | 3 +++
 modules/blast/blastn/main.nf                         | 3 +++
 modules/blast/makeblastdb/main.nf                    | 3 +++
 modules/bowtie/align/main.nf                         | 3 +++
 modules/bowtie/build/main.nf                         | 3 +++
 modules/bowtie2/align/main.nf                        | 3 +++
 modules/bowtie2/build/main.nf                        | 3 +++
 modules/bwa/aln/main.nf                              | 3 +++
 modules/bwa/index/main.nf                            | 3 +++
 modules/bwa/mem/main.nf                              | 3 +++
 modules/bwa/sampe/main.nf                            | 3 +++
 modules/bwa/samse/main.nf                            | 3 +++
 modules/bwamem2/index/main.nf                        | 3 +++
 modules/bwamem2/mem/main.nf                          | 3 +++
 modules/bwameth/align/main.nf                        | 3 +++
 modules/bwameth/index/main.nf                        | 3 +++
 modules/cat/cat/main.nf                              | 3 +++
 modules/cat/fastq/main.nf                            | 3 +++
 modules/cellranger/count/main.nf                     | 3 +++
 modules/cellranger/mkfastq/main.nf                   | 3 +++
 modules/cellranger/mkgtf/main.nf                     | 3 +++
 modules/cellranger/mkref/main.nf                     | 3 +++
 modules/checkm/lineagewf/main.nf                     | 3 +++
 modules/chromap/chromap/main.nf                      | 3 +++
 modules/chromap/index/main.nf                        | 3 +++
 modules/clonalframeml/main.nf                        | 3 +++
 modules/cmseq/polymut/main.nf                        | 3 +++
 modules/cnvkit/batch/main.nf                         | 3 +++
 modules/cooler/cload/main.nf                         | 3 +++
 modules/cooler/digest/main.nf                        | 3 +++
 modules/cooler/dump/main.nf                          | 3 +++
 modules/cooler/merge/main.nf                         | 3 +++
 modules/cooler/zoomify/main.nf                       | 3 +++
 modules/csvtk/concat/main.nf                         | 3 +++
 modules/csvtk/split/main.nf                          | 3 +++
 modules/custom/dumpsoftwareversions/main.nf          | 3 +++
 modules/custom/getchromsizes/main.nf                 | 3 +++
 modules/cutadapt/main.nf                             | 3 +++
 modules/damageprofiler/main.nf                       | 3 +++
 modules/dastool/dastool/main.nf                      | 3 +++
 modules/dastool/scaffolds2bin/main.nf                | 3 +++
 modules/dedup/main.nf                                | 3 +++
 modules/deeparg/downloaddata/main.nf                 | 3 +++
 modules/deeparg/predict/main.nf                      | 3 +++
 modules/deeptools/computematrix/main.nf              | 3 +++
 modules/deeptools/plotfingerprint/main.nf            | 3 +++
 modules/deeptools/plotheatmap/main.nf                | 3 +++
 modules/deeptools/plotprofile/main.nf                | 3 +++
 modules/deepvariant/main.nf                          | 3 +++
 modules/delly/call/main.nf                           | 3 +++
 modules/diamond/blastp/main.nf                       | 3 +++
 modules/diamond/blastx/main.nf                       | 3 +++
 modules/diamond/makedb/main.nf                       | 3 +++
 modules/dragmap/align/main.nf                        | 3 +++
 modules/dragmap/hashtable/main.nf                    | 3 +++
 modules/dragonflye/main.nf                           | 3 +++
 modules/dshbio/exportsegments/main.nf                | 3 +++
 modules/dshbio/filterbed/main.nf                     | 3 +++
 modules/dshbio/filtergff3/main.nf                    | 3 +++
 modules/dshbio/splitbed/main.nf                      | 3 +++
 modules/dshbio/splitgff3/main.nf                     | 3 +++
 modules/ectyper/main.nf                              | 3 +++
 modules/emmtyper/main.nf                             | 3 +++
 modules/ensemblvep/main.nf                           | 3 +++
 modules/expansionhunter/main.nf                      | 3 +++
 modules/fargene/main.nf                              | 3 +++
 modules/fastani/main.nf                              | 3 +++
 modules/fastp/main.nf                                | 3 +++
 modules/fastqc/main.nf                               | 3 +++
 modules/fastqscan/main.nf                            | 3 +++
 modules/fasttree/main.nf                             | 3 +++
 modules/fgbio/callmolecularconsensusreads/main.nf    | 3 +++
 modules/fgbio/fastqtobam/main.nf                     | 3 +++
 modules/fgbio/groupreadsbyumi/main.nf                | 3 +++
 modules/fgbio/sortbam/main.nf                        | 3 +++
 modules/filtlong/main.nf                             | 3 +++
 modules/flash/main.nf                                | 3 +++
 modules/freebayes/main.nf                            | 3 +++
 modules/gatk4/applybqsr/main.nf                      | 3 +++
 modules/gatk4/applyvqsr/main.nf                      | 3 +++
 modules/gatk4/baserecalibrator/main.nf               | 3 +++
 modules/gatk4/bedtointervallist/main.nf              | 3 +++
 modules/gatk4/calculatecontamination/main.nf         | 3 +++
 modules/gatk4/createsequencedictionary/main.nf       | 3 +++
 modules/gatk4/createsomaticpanelofnormals/main.nf    | 3 +++
 modules/gatk4/estimatelibrarycomplexity/main.nf      | 3 +++
 modules/gatk4/fastqtosam/main.nf                     | 3 +++
 modules/gatk4/filtermutectcalls/main.nf              | 3 +++
 modules/gatk4/gatherbqsrreports/main.nf              | 3 +++
 modules/gatk4/genomicsdbimport/main.nf               | 3 +++
 modules/gatk4/genotypegvcfs/main.nf                  | 3 +++
 modules/gatk4/getpileupsummaries/main.nf             | 3 +++
 modules/gatk4/haplotypecaller/main.nf                | 3 +++
 modules/gatk4/indexfeaturefile/main.nf               | 3 +++
 modules/gatk4/intervallisttools/main.nf              | 3 +++
 modules/gatk4/learnreadorientationmodel/main.nf      | 3 +++
 modules/gatk4/markduplicates/main.nf                 | 3 +++
 modules/gatk4/mergebamalignment/main.nf              | 3 +++
 modules/gatk4/mergevcfs/main.nf                      | 3 +++
 modules/gatk4/mutect2/main.nf                        | 3 +++
 modules/gatk4/revertsam/main.nf                      | 3 +++
 modules/gatk4/samtofastq/main.nf                     | 3 +++
 modules/gatk4/splitncigarreads/main.nf               | 3 +++
 modules/gatk4/variantfiltration/main.nf              | 3 +++
 modules/gatk4/variantrecalibrator/main.nf            | 3 +++
 modules/genmap/index/main.nf                         | 3 +++
 modules/genmap/mappability/main.nf                   | 3 +++
 modules/genrich/main.nf                              | 3 +++
 modules/gffread/main.nf                              | 3 +++
 modules/glnexus/main.nf                              | 3 +++
 modules/graphmap2/align/main.nf                      | 3 +++
 modules/graphmap2/index/main.nf                      | 3 +++
 modules/gstama/collapse/main.nf                      | 3 +++
 modules/gstama/merge/main.nf                         | 3 +++
 modules/gtdbtk/classifywf/main.nf                    | 3 +++
 modules/gubbins/main.nf                              | 3 +++
 modules/gunc/downloaddb/main.nf                      | 3 +++
 modules/gunc/run/main.nf                             | 3 +++
 modules/gunzip/main.nf                               | 3 +++
 modules/hicap/main.nf                                | 3 +++
 modules/hifiasm/main.nf                              | 3 +++
 modules/hisat2/align/main.nf                         | 3 +++
 modules/hisat2/build/main.nf                         | 3 +++
 modules/hisat2/extractsplicesites/main.nf            | 3 +++
 modules/hmmcopy/gccounter/main.nf                    | 3 +++
 modules/hmmcopy/generatemap/main.nf                  | 3 +++
 modules/hmmcopy/mapcounter/main.nf                   | 3 +++
 modules/hmmcopy/readcounter/main.nf                  | 3 +++
 modules/hmmer/hmmalign/main.nf                       | 3 +++
 modules/homer/annotatepeaks/main.nf                  | 3 +++
 modules/homer/findpeaks/main.nf                      | 3 +++
 modules/homer/maketagdirectory/main.nf               | 3 +++
 modules/homer/makeucscfile/main.nf                   | 3 +++
 modules/idr/main.nf                                  | 3 +++
 modules/imputeme/vcftoprs/main.nf                    | 3 +++
 modules/iqtree/main.nf                               | 3 +++
 modules/ismapper/main.nf                             | 3 +++
 modules/isoseq3/cluster/main.nf                      | 3 +++
 modules/isoseq3/refine/main.nf                       | 3 +++
 modules/ivar/consensus/main.nf                       | 3 +++
 modules/ivar/trim/main.nf                            | 3 +++
 modules/ivar/variants/main.nf                        | 3 +++
 modules/jupyternotebook/main.nf                      | 3 +++
 modules/kallisto/index/main.nf                       | 3 +++
 modules/kallistobustools/count/main.nf               | 3 +++
 modules/kallistobustools/ref/main.nf                 | 3 +++
 modules/khmer/normalizebymedian/main.nf              | 3 +++
 modules/kleborate/main.nf                            | 3 +++
 modules/kraken2/kraken2/main.nf                      | 3 +++
 modules/krona/kronadb/main.nf                        | 3 +++
 modules/krona/ktimporttaxonomy/main.nf               | 3 +++
 modules/last/dotplot/main.nf                         | 3 +++
 modules/last/lastal/main.nf                          | 3 +++
 modules/last/lastdb/main.nf                          | 3 +++
 modules/last/mafconvert/main.nf                      | 3 +++
 modules/last/mafswap/main.nf                         | 3 +++
 modules/last/postmask/main.nf                        | 3 +++
 modules/last/split/main.nf                           | 3 +++
 modules/last/train/main.nf                           | 3 +++
 modules/leehom/main.nf                               | 3 +++
 modules/lima/main.nf                                 | 3 +++
 modules/lissero/main.nf                              | 3 +++
 modules/lofreq/call/main.nf                          | 3 +++
 modules/lofreq/callparallel/main.nf                  | 3 +++
 modules/lofreq/filter/main.nf                        | 3 +++
 modules/lofreq/indelqual/main.nf                     | 3 +++
 modules/macrel/contigs/main.nf                       | 3 +++
 modules/macs2/callpeak/main.nf                       | 3 +++
 modules/malt/build/main.nf                           | 3 +++
 modules/malt/run/main.nf                             | 3 +++
 modules/maltextract/main.nf                          | 3 +++
 modules/manta/germline/main.nf                       | 3 +++
 modules/manta/somatic/main.nf                        | 3 +++
 modules/manta/tumoronly/main.nf                      | 3 +++
 modules/mapdamage2/main.nf                           | 3 +++
 modules/mash/dist/main.nf                            | 3 +++
 modules/mash/sketch/main.nf                          | 3 +++
 modules/mashtree/main.nf                             | 3 +++
 modules/maxbin2/main.nf                              | 3 +++
 modules/medaka/main.nf                               | 3 +++
 modules/megahit/main.nf                              | 3 +++
 modules/meningotype/main.nf                          | 3 +++
 modules/metabat2/jgisummarizebamcontigdepths/main.nf | 3 +++
 modules/metabat2/metabat2/main.nf                    | 3 +++
 modules/metaphlan3/main.nf                           | 3 +++
 modules/methyldackel/extract/main.nf                 | 3 +++
 modules/methyldackel/mbias/main.nf                   | 3 +++
 modules/minia/main.nf                                | 3 +++
 modules/miniasm/main.nf                              | 3 +++
 modules/minimap2/align/main.nf                       | 3 +++
 modules/minimap2/index/main.nf                       | 3 +++
 modules/mlst/main.nf                                 | 3 +++
 modules/mosdepth/main.nf                             | 3 +++
 modules/msisensor/msi/main.nf                        | 3 +++
 modules/msisensor/scan/main.nf                       | 3 +++
 modules/mtnucratio/main.nf                           | 3 +++
 modules/multiqc/main.nf                              | 3 +++
 modules/mummer/main.nf                               | 3 +++
 modules/muscle/main.nf                               | 3 +++
 modules/nanolyse/main.nf                             | 3 +++
 modules/nanoplot/main.nf                             | 3 +++
 modules/ncbigenomedownload/main.nf                   | 3 +++
 modules/nextclade/datasetget/main.nf                 | 3 +++
 modules/nextclade/run/main.nf                        | 3 +++
 modules/ngmaster/main.nf                             | 3 +++
 modules/nucmer/main.nf                               | 3 +++
 modules/optitype/main.nf                             | 3 +++
 modules/pairix/main.nf                               | 3 +++
 modules/pairtools/dedup/main.nf                      | 3 +++
 modules/pairtools/flip/main.nf                       | 3 +++
 modules/pairtools/parse/main.nf                      | 3 +++
 modules/pairtools/restrict/main.nf                   | 3 +++
 modules/pairtools/select/main.nf                     | 3 +++
 modules/pairtools/sort/main.nf                       | 3 +++
 modules/pangolin/main.nf                             | 3 +++
 modules/paraclu/main.nf                              | 3 +++
 modules/pbbam/pbmerge/main.nf                        | 3 +++
 modules/pbccs/main.nf                                | 3 +++
 modules/peddy/main.nf                                | 3 +++
 modules/phantompeakqualtools/main.nf                 | 3 +++
 modules/phyloflash/main.nf                           | 3 +++
 modules/picard/collecthsmetrics/main.nf              | 3 +++
 modules/picard/collectmultiplemetrics/main.nf        | 3 +++
 modules/picard/collectwgsmetrics/main.nf             | 3 +++
 modules/picard/filtersamreads/main.nf                | 3 +++
 modules/picard/markduplicates/main.nf                | 3 +++
 modules/picard/mergesamfiles/main.nf                 | 3 +++
 modules/picard/sortsam/main.nf                       | 3 +++
 modules/pirate/main.nf                               | 3 +++
 modules/plasmidid/main.nf                            | 3 +++
 modules/plink/extract/main.nf                        | 3 +++
 modules/plink/vcf/main.nf                            | 3 +++
 modules/plink2/extract/main.nf                       | 3 +++
 modules/plink2/vcf/main.nf                           | 3 +++
 modules/pmdtools/filter/main.nf                      | 3 +++
 modules/porechop/main.nf                             | 3 +++
 modules/preseq/lcextrap/main.nf                      | 3 +++
 modules/prodigal/main.nf                             | 3 +++
 modules/prokka/main.nf                               | 3 +++
 modules/pycoqc/main.nf                               | 3 +++
 modules/pydamage/analyze/main.nf                     | 3 +++
 modules/pydamage/filter/main.nf                      | 3 +++
 modules/qcat/main.nf                                 | 3 +++
 modules/qualimap/bamqc/main.nf                       | 3 +++
 modules/qualimap/rnaseq/main.nf                      | 3 +++
 modules/quast/main.nf                                | 3 +++
 modules/racon/main.nf                                | 3 +++
 modules/rapidnj/main.nf                              | 3 +++
 modules/rasusa/main.nf                               | 3 +++
 modules/raven/main.nf                                | 3 +++
 modules/raxmlng/main.nf                              | 3 +++
 modules/rmarkdownnotebook/main.nf                    | 3 +++
 modules/roary/main.nf                                | 3 +++
 modules/rsem/calculateexpression/main.nf             | 3 +++
 modules/rsem/preparereference/main.nf                | 3 +++
 modules/rseqc/bamstat/main.nf                        | 3 +++
 modules/rseqc/inferexperiment/main.nf                | 3 +++
 modules/rseqc/innerdistance/main.nf                  | 3 +++
 modules/rseqc/junctionannotation/main.nf             | 3 +++
 modules/rseqc/junctionsaturation/main.nf             | 3 +++
 modules/rseqc/readdistribution/main.nf               | 3 +++
 modules/rseqc/readduplication/main.nf                | 3 +++
 modules/rseqc/tin/main.nf                            | 3 +++
 modules/salmon/index/main.nf                         | 3 +++
 modules/salmon/quant/main.nf                         | 3 +++
 modules/samblaster/main.nf                           | 3 +++
 modules/samtools/ampliconclip/main.nf                | 3 +++
 modules/samtools/bam2fq/main.nf                      | 3 +++
 modules/samtools/depth/main.nf                       | 3 +++
 modules/samtools/faidx/main.nf                       | 3 +++
 modules/samtools/fastq/main.nf                       | 3 +++
 modules/samtools/fixmate/main.nf                     | 3 +++
 modules/samtools/flagstat/main.nf                    | 3 +++
 modules/samtools/idxstats/main.nf                    | 3 +++
 modules/samtools/index/main.nf                       | 3 +++
 modules/samtools/merge/main.nf                       | 3 +++
 modules/samtools/mpileup/main.nf                     | 3 +++
 modules/samtools/sort/main.nf                        | 3 +++
 modules/samtools/stats/main.nf                       | 3 +++
 modules/samtools/view/main.nf                        | 3 +++
 modules/scoary/main.nf                               | 3 +++
 modules/seacr/callpeak/main.nf                       | 3 +++
 modules/seqkit/split2/main.nf                        | 3 +++
 modules/seqsero2/main.nf                             | 3 +++
 modules/seqtk/mergepe/main.nf                        | 3 +++
 modules/seqtk/sample/main.nf                         | 3 +++
 modules/seqtk/subseq/main.nf                         | 3 +++
 modules/sequenzautils/bam2seqz/main.nf               | 3 +++
 modules/sequenzautils/gcwiggle/main.nf               | 3 +++
 modules/seqwish/induce/main.nf                       | 3 +++
 modules/shovill/main.nf                              | 3 +++
 modules/snpdists/main.nf                             | 3 +++
 modules/snpeff/main.nf                               | 3 +++
 modules/snpsift/split/main.nf                        | 3 +++
 modules/snpsites/main.nf                             | 3 +++
 modules/sortmerna/main.nf                            | 3 +++
 modules/spades/main.nf                               | 3 +++
 modules/spatyper/main.nf                             | 3 +++
 modules/sratools/fasterqdump/main.nf                 | 3 +++
 modules/sratools/prefetch/main.nf                    | 3 +++
 modules/staphopiasccmec/main.nf                      | 3 +++
 modules/star/align/main.nf                           | 3 +++
 modules/star/genomegenerate/main.nf                  | 3 +++
 modules/strelka/germline/main.nf                     | 3 +++
 modules/strelka/somatic/main.nf                      | 3 +++
 modules/stringtie/merge/main.nf                      | 3 +++
 modules/stringtie/stringtie/main.nf                  | 3 +++
 modules/subread/featurecounts/main.nf                | 3 +++
 modules/svdb/query/main.nf                           | 3 +++
 modules/tabix/bgzip/main.nf                          | 3 +++
 modules/tabix/bgziptabix/main.nf                     | 3 +++
 modules/tabix/tabix/main.nf                          | 3 +++
 modules/tbprofiler/profile/main.nf                   | 3 +++
 modules/tiddit/cov/main.nf                           | 3 +++
 modules/tiddit/sv/main.nf                            | 3 +++
 modules/transdecoder/longorf/main.nf                 | 3 +++
 modules/transdecoder/predict/main.nf                 | 3 +++
 modules/trimgalore/main.nf                           | 3 +++
 modules/ucsc/bed12tobigbed/main.nf                   | 3 +++
 modules/ucsc/bedclip/main.nf                         | 3 +++
 modules/ucsc/bedgraphtobigwig/main.nf                | 3 +++
 modules/ucsc/bigwigaverageoverbed/main.nf            | 3 +++
 modules/ucsc/liftover/main.nf                        | 3 +++
 modules/ucsc/wigtobigwig/main.nf                     | 3 +++
 modules/ultra/pipeline/main.nf                       | 3 +++
 modules/umitools/dedup/main.nf                       | 3 +++
 modules/umitools/extract/main.nf                     | 3 +++
 modules/unicycler/main.nf                            | 3 +++
 modules/untar/main.nf                                | 3 +++
 modules/unzip/main.nf                                | 3 +++
 modules/variantbam/main.nf                           | 3 +++
 modules/vcfanno/main.nf                              | 3 +++
 modules/vcflib/vcfuniq/main.nf                       | 3 +++
 modules/vcftools/main.nf                             | 3 +++
 modules/yara/index/main.nf                           | 3 +++
 modules/yara/mapper/main.nf                          | 3 +++
 386 files changed, 1158 insertions(+)

diff --git a/modules/abacas/main.nf b/modules/abacas/main.nf
index 490402142e42..00c9169f5c73 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 0cf257ffeaf7..55c5f17c1e7e 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 ?: "${meta.id}"
diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf
index aff72abc1c22..8503505d1457 100644
--- a/modules/agrvate/main.nf
+++ b/modules/agrvate/main.nf
@@ -15,6 +15,9 @@ process AGRVATE {
     path "${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 850a018ff00e..b2cb1b0c0eb2 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 871b57c685a0..57cdcff8f12f 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 0fcb6ba744fb..e0d30b45aba4 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 780f51113009..8e6b2879d849 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 c25ec0db09e4..af74b1326529 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 56541222d9bc..889f92a9c5e1 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 fbd623f4b3ae..952aaed49ca4 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 ?: "${meta.id}"
diff --git a/modules/bakta/main.nf b/modules/bakta/main.nf
index 2582dac23c8e..95e87899b517 100644
--- a/modules/bakta/main.nf
+++ b/modules/bakta/main.nf
@@ -25,6 +25,9 @@ process BAKTA {
     tuple val(meta), path("${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 88fe21aa64a6..922b72e68458 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 54416323b056..f45b73d872ee 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 141e762d3b1e..b993aad1ad8a 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 8d5e5690f1fb..014e5cdba900 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 9ceb2b651bec..514ea4c0757f 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 bc2a94951962..ee504a129d91 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 ac8394975726..914399c5a53e 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 79c3c30631e0..0ae005e40655 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 0c916dfe8990..b55929ce92bc 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 4c02f84ead13..fdd6d1020087 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 d02e7605bbdd..c0633ef73f96 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 040e65343ef9..a0c436e2d1cc 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 98b422b1b46a..82961e3212bb 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 e5275003eac8..548a9277bc3c 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 ?: "${meta.id}"
diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf
index fdde3022bf4f..c8f89753a9c2 100644
--- a/modules/bcftools/isec/main.nf
+++ b/modules/bcftools/isec/main.nf
@@ -14,6 +14,9 @@ process BCFTOOLS_ISEC {
     tuple val(meta), path("${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 f1c02e8deeca..7bee5a9bd3b7 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 cdd38eeca331..676eae7a4fd6 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 e8bf63243902..cd681f21e282 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 a165b103fb4f..8921abddef4c 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 e6d9025da9d0..7d2abecfc104 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 2fcadc988dfe..8478fe252eb3 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 54a28bce4220..7e150d1fe1c3 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 7056ecdb1ed1..2a240f4a99b6 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 98d9ea2f188a..fd782deca661 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 3146827c9b10..8c8e7efaa330 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 ?: "${meta.id}"
diff --git a/modules/bedtools/genomecov/main.nf b/modules/bedtools/genomecov/main.nf
index ca491e7586fa..4804d40a5512 100644
--- a/modules/bedtools/genomecov/main.nf
+++ b/modules/bedtools/genomecov/main.nf
@@ -16,6 +16,9 @@ process BEDTOOLS_GENOMECOV {
     tuple val(meta), path("*.${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 5a283e94fb26..4ce8c01eb5cb 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 ?: "${bed.baseName}"
diff --git a/modules/bedtools/intersect/main.nf b/modules/bedtools/intersect/main.nf
index afb0d056d583..29f16adbc3f5 100644
--- a/modules/bedtools/intersect/main.nf
+++ b/modules/bedtools/intersect/main.nf
@@ -15,6 +15,9 @@ process BEDTOOLS_INTERSECT {
     tuple val(meta), path("*.${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 2414393c0a9e..2a19226c8215 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 7eeb4c7dbb67..04ba116ba842 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 5f1da95bc160..6d1daa035900 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 9d8633ec0443..ae4f81cc11c4 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 ?: "${meta.id}"
diff --git a/modules/bedtools/sort/main.nf b/modules/bedtools/sort/main.nf
index 1ed95a57f43e..43dc9bdabac2 100644
--- a/modules/bedtools/sort/main.nf
+++ b/modules/bedtools/sort/main.nf
@@ -15,6 +15,9 @@ process BEDTOOLS_SORT {
     tuple val(meta), path("*.${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 b2efefe51dee..8e2b42c5069c 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 e490b48c97a1..eeddcabb2ba1 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 16c624f1e35e..ea763774aaf8 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 e096b2b8ae40..59c495c5196b 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 d99c2b5e3032..5543ab7e8cb6 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 f828ecd8ed88..bec3de99ea35 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 72dba72e9de3..49fec53e24f9 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 3a0bafe07618..b85f6c8ecb76 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 b4c426a45534..12208ea89c62 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 b25b5e21a5f4..ba82b67de3c3 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 dbbc8efabdc5..e01d9855d16d 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 20b08f72105e..7e8a9659bd96 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 da2e9ed52a62..a4da62d073b5 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 992e25de5f82..741c01596aec 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 891027377876..3affbf16bc36 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 9695bd2dca1e..9a91c77f2dde 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 0b5ec2556142..e781679e89ef 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 bee06bc8fc39..ac04c7397ae4 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 e00538c919f8..0e9cc2f8ba14 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 6d4d8028edc0..56f595ec6cf0 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 0bcd9bace8a1..6d9c4431826c 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 f5b8ff59f081..4c1068268ae8 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 2efe20a50d37..4ee4459943d9 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 d02598e1f370..bf0877c3e867 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 ?: "${meta.id}"
diff --git a/modules/cellranger/count/main.nf b/modules/cellranger/count/main.nf
index 63fac70940c0..6a206b6e1488 100644
--- a/modules/cellranger/count/main.nf
+++ b/modules/cellranger/count/main.nf
@@ -15,6 +15,9 @@ process CELLRANGER_COUNT {
     path("sample-${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 f47aa75ca339..9c023bcac837 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 4342fd00fc7b..9dc2fe1ae563 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 d38d6809f444..11cf80e3629d 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 992b165ec7bb..d92f2c788ba6 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 67384b0ca07c..cdbf6049e973 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 61bcee108535..52deaf06ccf1 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 db647a38e161..24502796b9ec 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 47e86f0cf9d0..a02551c827bc 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 811cb4090c57..7c44d9f614cc 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 d8bdc0316502..52964b8dd931 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 9658ec3102e4..7e8e36f0b02d 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 a438acc868b7..996e9b5bfbcd 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 b1814b689e60..1e439cafbb8d 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 226d41141de9..942282c0d6a8 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 ?: "${meta.id}"
diff --git a/modules/csvtk/concat/main.nf b/modules/csvtk/concat/main.nf
index 94b1925a56a4..f30e8332a0e9 100644
--- a/modules/csvtk/concat/main.nf
+++ b/modules/csvtk/concat/main.nf
@@ -16,6 +16,9 @@ process CSVTK_CONCAT {
     tuple val(meta), path("${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 ?: "${meta.id}"
diff --git a/modules/csvtk/split/main.nf b/modules/csvtk/split/main.nf
index 52ab7ec7ceaf..5653d192a3fe 100644
--- a/modules/csvtk/split/main.nf
+++ b/modules/csvtk/split/main.nf
@@ -16,6 +16,9 @@ process CSVTK_SPLIT {
     tuple val(meta), path("*.${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 934bb467238f..327d5100560d 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 270b3f4893a8..39da7d34e93d 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 74c42768da8c..9b310c0e6932 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 ?: "${meta.id}"
diff --git a/modules/damageprofiler/main.nf b/modules/damageprofiler/main.nf
index 23eb9397b145..4b146e7f3841 100644
--- a/modules/damageprofiler/main.nf
+++ b/modules/damageprofiler/main.nf
@@ -17,6 +17,9 @@ process DAMAGEPROFILER {
     tuple val(meta), path("${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 722f6c5554f7..53dfea199217 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 09f800bb219e..6e9fcdc296ac 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 8b4bdc3711a1..c612ec143059 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 cc420e6a9db6..aacdc7787b3c 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 9408fa3da9c4..3e478e59d167 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 70be934bfcdd..96dfef3c6029 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 7925c9a9702e..83613be7b3d7 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 992c90583019..1e402e3919cd 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 60184fa6bbb8..d83a9493876a 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 98345c836c46..c5e819973c57 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 fc04cda7f6d6..d639ee160b19 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 c7342767cedb..955952dcdfac 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 bd7d1dd99db9..3700bd36dccc 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 ?: "${meta.id}"
diff --git a/modules/diamond/makedb/main.nf b/modules/diamond/makedb/main.nf
index cccfcce97b57..e3d62f00763f 100644
--- a/modules/diamond/makedb/main.nf
+++ b/modules/diamond/makedb/main.nf
@@ -16,6 +16,9 @@ process DIAMOND_MAKEDB {
     path "${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 8a6f082a0607..9f261cc2e754 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 ab55364b8a67..81333dfdae18 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 8ca988327afc..1459714366bb 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 0a1920a6a9ea..49442f819055 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 6efe07e8dc54..7e3da24e7c7a 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 5214ce23efd8..0539bbe041ae 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 c0ca6a8b2b94..824c7e4d08d0 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 012afec7e747..424bc3681cc5 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 0e040958edcb..34973ee6c9b7 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 70dabfb7a9a6..955cc3085870 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 e3d0c286d9bc..c2bd055fa27e 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 4db78230d080..4e62b2a63503 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 ?: "${meta.id}"
diff --git a/modules/fargene/main.nf b/modules/fargene/main.nf
index 73bdd41133eb..029f6065aa88 100644
--- a/modules/fargene/main.nf
+++ b/modules/fargene/main.nf
@@ -31,6 +31,9 @@ process FARGENE {
     tuple val(meta), path("${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 cc1c49028ffa..e6b44a8296f1 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 a406036a7575..d8218350cf2f 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 d250eca07586..ed6b8c50b1fb 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 a0dcc46a9c91..4cca0317e38f 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 5e57aae9ccce..ce65846a6c94 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 3aab935be010..347dc269e5c5 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 3060d7153f02..329aff331769 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 47f000a59945..31250d23ce82 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 c542f3df494b..5026987cb8e9 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 ?: "${meta.id}"
diff --git a/modules/filtlong/main.nf b/modules/filtlong/main.nf
index bb1c1eb31fb6..0e6fdd5362fc 100644
--- a/modules/filtlong/main.nf
+++ b/modules/filtlong/main.nf
@@ -14,6 +14,9 @@ process FILTLONG {
     tuple val(meta), path("${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 7bc38c971be8..bb6f249970bc 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 d462088a9ef4..e67e4c720604 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 c246190ae4ae..672e93e045cc 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 992339752010..006840b37cc4 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 42391d629499..48c127f0eefb 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 37f46f4851b5..9f2b2dfe7a64 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 f4e98f645b01..177f4878cf04 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 2cbd89484d95..714843c273af 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 8ab578c4db03..a82c24d8028b 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 744ebf218fb5..2894e305bc23 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 f0116b41ede2..631c0394f43d 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 2f5f8dcb5d9e..a7dd9a61a9c4 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 b084ab00b96b..f8d91a920bbd 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 94a589cd4087..e88471e18606 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 016da1f5b019..c3e41229d616 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 a81ae6358602..3667a2108d22 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 8c22da688229..6f03ffd2cc76 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 ecd24173b9cf..b5add0e0c94e 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 174121604ef4..40c7fb19a2f0 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 d1bce19f2f98..7d96c27e0a0f 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 c101d042dad9..735b093ee9cc 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 0e294454f765..e636e1cdcfc6 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 b2e584a8c7a9..3e9973e7dcb3 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 c33cee18ea8d..1c8c399312a8 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 5a13d61d0089..23f99ab438f8 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 0a75f604daab..2da40b6c44c4 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 29483fb555a4..6d0a35fde442 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 beaec0c0c489..3a41d20cb518 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 c4aa5535869a..df8a959995ae 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 943f1a31ef3b..a19c661934ac 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 94083f148994..50a174931b4f 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 d9deea3cc4c3..d276c4107809 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 e7893f8ba7d1..7c575c97ff20 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 b8afca223497..84da95a04a84 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 554e585b0ee9..8834cc0ab669 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 fffc7bcbcbf3..ef240b6c05ac 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 1c06692d3b49..36d8a311e02b 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 53ff93e47d55..221ec3c9fdeb 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 ?: "${meta.id}"
diff --git a/modules/gtdbtk/classifywf/main.nf b/modules/gtdbtk/classifywf/main.nf
index 009efa8d1cac..bf83c2ad9a64 100644
--- a/modules/gtdbtk/classifywf/main.nf
+++ b/modules/gtdbtk/classifywf/main.nf
@@ -25,6 +25,9 @@ process GTDBTK_CLASSIFYWF {
     path "gtdbtk.${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 b4c6dc235d2a..17a271d8f766 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 430b862b9b83..006386933af1 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 8508c9f005ed..ce9bd7c67c2b 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 ?: "${meta.id}"
diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf
index 77a4e546bfd9..9d4b06669f99 100644
--- a/modules/gunzip/main.nf
+++ b/modules/gunzip/main.nf
@@ -14,6 +14,9 @@ process GUNZIP {
     tuple val(meta), path("$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 a96343f63a35..51fe0b83db7f 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 208554d6ef11..ea7c4976d2a2 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 ae88861693f8..7f6800189401 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 4e8cd02bb994..50f65e3a1558 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 302c35f1f329..941359779528 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 a1de8b974ed5..3911df6b4f27 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 1d248853a831..c6c087251494 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 ab20868eef46..b369d12baeb6 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 a6e89f9139cf..ff13770d8e30 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 e6d04044d2c2..d3df3c893779 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 84e0241a4735..c9da82ed4d7c 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 66de06b6d8bf..b9947774eb5f 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 72e2091f8082..262998d59dd3 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 17e86947f99b..c82435ea1408 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 7e3778787ada..d18ef2ebc513 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 5fee90c29dd0..8ce3f73d03b7 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 54a6486d0138..db394bd28977 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 a51cc01ef96e..a2c79115849f 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 fdd47971a1ab..fe1b10d4ae30 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 5044cba23562..2501481100e0 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 96d00ce2127b..db6301e90669 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 4d0c70a2caa8..819aa5dd103d 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 bb6e402bd768..85c4cacd0a44 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 871d6ccdf9bd..baed502c3716 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 4dc9c6d050cb..0f10e564637c 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 d67eba318330..d674aece2ff7 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 1e496f6735bf..1e7896154c29 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 50b3d603e639..f89b2585b6ee 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 4a7937936f96..88cbc951b91e 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 eaabb2297678..3ec5df52d3f1 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 d815603563af..afcb06947e9e 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 bc79c98cb038..7837bb876922 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 e88574031c9e..a71d001aea1d 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 b5ac8bfe508a..882b16cd0f21 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 e9895c5cacff..0747ba4dc063 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 ca60e7fe8c5c..8ffec2f92289 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 0a58b027b5b5..55f6a1a96930 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 ca981e1c9391..6bc649303f7a 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 60ed135b3479..433eff0c49b8 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 471db7c1afea..23f4f36bd350 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 b5cb2dcb30aa..906d094e6823 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 691e43f2a93e..e98fd157f70a 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 667697ef01d0..29995db8307d 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 d7fd078bddcd..773bc21244bc 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 764efcc5071a..4dffc302a9ee 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 34a5aef8e1c4..bddc012f8fdf 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 5e5b8f44f6a3..ac53d70fc7e2 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 558ef6e89229..65db4d3e8e0d 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 c5c88f8e0921..9aaf97a93be5 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 d1b0c4270867..8eeb304bf9ad 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 5e81667e7bb5..99657305eb74 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 e3a42016ac2a..75710141780f 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 2a8c0acc7a26..fab789ece4ea 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 1d62635b0ab4..886a8fb9bbb8 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 63f7a840308f..3d52b16e2580 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 e3668fda0345..53007115541d 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 323bd3397ee9..270767b56824 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 d93641f7e059..54263af775d6 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 5da2f8058bd4..4cd9af1929e2 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 4d384391fdd6..7b818d004a0e 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 761b1c34f94f..da77d0f0d415 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 7b5118839d85..6e6a1ad1030e 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 c3b65b9d0d2c..24c3002956a9 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 4a5869b6f962..7125eeb22eba 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 a8af0ae9b75c..23ebe19a2dd4 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 64965af3d20c..3fc6b277d7a9 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 a39c0305d94e..b42420734f40 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 021f76f17a28..755e62f88c07 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 968cafa58444..87dd74f9aaa9 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 b0db6925f861..f77b10f2225b 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 500250e97a9c..fe06f14d7266 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 10cdd142d24d..3dfeb861360d 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 b2983b82bdc5..65396548be56 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 d2669b7e14ef..cc7bc86b1009 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 ?: "${meta.id}"
diff --git a/modules/msisensor/msi/main.nf b/modules/msisensor/msi/main.nf
index 398b34a6b854..954c5bec3983 100644
--- a/modules/msisensor/msi/main.nf
+++ b/modules/msisensor/msi/main.nf
@@ -17,6 +17,9 @@ process MSISENSOR_MSI {
     tuple val(meta), path("${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 223b4f441295..399513cec884 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 83d6ea2b49fb..cb8d27e38804 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 3dceb162a38e..0ff7cac11fe5 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 39ad3e8bcad6..1fe91404eeca 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 6d549aaac2b5..b2a1a13135c1 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 0ad0f799d1aa..2b4f0928aaee 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 c3fb8a373b50..083e23747ac9 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 9897c8613bee..60323dc88664 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 ?: "${meta.id}"
diff --git a/modules/nextclade/datasetget/main.nf b/modules/nextclade/datasetget/main.nf
index 75bb88f3eae2..4dd82ee355be 100644
--- a/modules/nextclade/datasetget/main.nf
+++ b/modules/nextclade/datasetget/main.nf
@@ -16,6 +16,9 @@ process NEXTCLADE_DATASETGET {
     path "$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 ?: "${dataset}"
diff --git a/modules/nextclade/run/main.nf b/modules/nextclade/run/main.nf
index b3d101ce4fb4..4d4bdb88b170 100644
--- a/modules/nextclade/run/main.nf
+++ b/modules/nextclade/run/main.nf
@@ -18,6 +18,9 @@ process NEXTCLADE_RUN {
     tuple val(meta), path("${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 7d04031c893b..ef288e8f5647 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 4e296515977a..5b70abd92698 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 ?: "${meta.id}"
diff --git a/modules/optitype/main.nf b/modules/optitype/main.nf
index d27f7f9ffca3..984d466954ff 100644
--- a/modules/optitype/main.nf
+++ b/modules/optitype/main.nf
@@ -14,6 +14,9 @@ process OPTITYPE {
     tuple val(meta), path("${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 c1b9658cb0ad..0b8c63c60fb9 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 fe59e155f93c..2c171e7a6389 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 376191ced668..4959c4eef253 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 7bd778c953fb..190346b13537 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 8759f7093ab4..59e18648c8bb 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 a6d62ba70896..9d434884ed4b 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 d5996dd0a6af..15ed56d1a83d 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 6c8682e3ae91..9fbc69b8f2ea 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 cc16674e8c90..1dcc4f90c3b3 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 e0525cb1c1d4..aa0ca78882fd 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 440fbc727588..5bfae1bf31c7 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 1aa02a4f1be9..50cdc698349a 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 6fe34cc28b70..c8325b05991d 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 ?: "${meta.id}"
diff --git a/modules/phyloflash/main.nf b/modules/phyloflash/main.nf
index 9ebc40dee5b9..23c38d56cb6d 100644
--- a/modules/phyloflash/main.nf
+++ b/modules/phyloflash/main.nf
@@ -16,6 +16,9 @@ process PHYLOFLASH {
     tuple val(meta), path("${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 ae3e4d96c35b..07e8504f2a80 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 9511f7a4f5c4..e023ea3c2996 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 dd9da1b63af9..f4efaa4ce934 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 6a9c9c72778b..ab75abfa3fa4 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 7990d7e6a2b9..5196b6edf7ae 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 96616a44f899..ef5c3980721c 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 6676eed6d923..adec17cba6b2 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 c7d7476c5ad9..20544a1bdf2e 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 ?: "${meta.id}"
diff --git a/modules/plasmidid/main.nf b/modules/plasmidid/main.nf
index 7404a678abb7..7911d8068997 100644
--- a/modules/plasmidid/main.nf
+++ b/modules/plasmidid/main.nf
@@ -22,6 +22,9 @@ process PLASMIDID {
     tuple val(meta), path("${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 688ada678d52..fa22b527f5a7 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 719e90d2a0f9..0a69a021f749 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 7eb24abc9026..89cffdc342db 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 078ece1ec367..041cb4b997fa 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 b647b6d362a3..2d9d6eb3e9d5 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 f5ad93f846da..65982b8b9e84 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 b5bd06206f50..d6dd19e231c9 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 ?: "${meta.id}"
diff --git a/modules/prodigal/main.nf b/modules/prodigal/main.nf
index 6324893142b3..5768952b7fff 100644
--- a/modules/prodigal/main.nf
+++ b/modules/prodigal/main.nf
@@ -18,6 +18,9 @@ process PRODIGAL {
     tuple val(meta), path("${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 ?: "${meta.id}"
diff --git a/modules/prokka/main.nf b/modules/prokka/main.nf
index 551a17b9c864..3e46d1a19674 100644
--- a/modules/prokka/main.nf
+++ b/modules/prokka/main.nf
@@ -27,6 +27,9 @@ process PROKKA {
     tuple val(meta), path("${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 e966b31c7457..a5e6fcb20238 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 c06c592ccde2..39e01fa1eb26 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 ab0b211543f2..a748875a2c6d 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 7d81952d0a40..4c75b00359e0 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 ?: "${meta.id}"
diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf
index 973fd6a4c700..4bff0254e09f 100644
--- a/modules/qualimap/bamqc/main.nf
+++ b/modules/qualimap/bamqc/main.nf
@@ -16,6 +16,9 @@ process QUALIMAP_BAMQC {
     tuple val(meta), path("${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 ?: "${meta.id}"
diff --git a/modules/qualimap/rnaseq/main.nf b/modules/qualimap/rnaseq/main.nf
index d83fcd99991a..3b2f88adec42 100644
--- a/modules/qualimap/rnaseq/main.nf
+++ b/modules/qualimap/rnaseq/main.nf
@@ -15,6 +15,9 @@ process QUALIMAP_RNASEQ {
     tuple val(meta), path("${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 e88051b55cfa..beb797d4449a 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 9be5ce63386c..6f8448967f95 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 04a082279cc2..952bae4c3e44 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 c2893d1843fb..47c8ece6179c 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 0d81b94b4a89..8bcf6bb1791e 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 62b6c78a17ba..e872a4e61ab3 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 18d8e150e71b..336b0af00f95 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 edda3281d031..fabb3234fddd 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 ?: "${meta.id}"
diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf
index 4b2ada47a970..cf147a633a3e 100644
--- a/modules/rsem/calculateexpression/main.nf
+++ b/modules/rsem/calculateexpression/main.nf
@@ -22,6 +22,9 @@ process RSEM_CALCULATEEXPRESSION {
     tuple val(meta), path("${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 a5b8922a0b60..2d2ca2056025 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 1141a13f2cf1..958221fdeed7 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 2243c43e15be..23c1b6882747 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 425737d68ede..b05661de175f 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 d2562e5cb956..c3401dc51a56 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 695762b5cdc7..11b629040bc5 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 333193e307d5..3198c5c6660c 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 134f2e8dba95..cb989a5f2027 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 b7bff0f318db..da58fc06bc68 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 b0a2f973cd86..737087f968e4 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 '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
diff --git a/modules/salmon/quant/main.nf b/modules/salmon/quant/main.nf
index 6cae4f72d644..bd4792c52e6f 100644
--- a/modules/salmon/quant/main.nf
+++ b/modules/salmon/quant/main.nf
@@ -19,6 +19,9 @@ process SALMON_QUANT {
     tuple val(meta), path("${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 4627b978d725..c881389acd9a 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 e553f218419a..69c2ff7bde75 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 32588dd7f88c..4b78a46e32c4 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 50b2ed5d1728..d68c5adf1f92 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 58c445d8a4cb..b83a4952d86c 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 a2dae0873701..7eb60117b22c 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 89ac666d29d9..c1a8164b4d8b 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 119adf7752ab..c267922b3e49 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 fc54e6761aeb..8a057413ed2f 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 c4fa2c63f9b7..dfe0234f7c1d 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 a318bfc4410b..be6fe32ebc59 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 c40f46d1d0ad..77afae60a7f7 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 42c7bbf45d22..0f2237cc1816 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 7209070d9e27..f6fe3bfef84f 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 cb205d0b72de..aee21a4eaecc 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 ca33041d22d9..cfa58ab23e55 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 12b9205ff742..340c0eef36a9 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 5bed1daebf26..ff91d86bd95b 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 0a7aa6ad76aa..a5393cf63b32 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 299c9ea4dcf5..519a4ab95ed2 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 96e08fd48556..a9a893705579 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 abfe4faa2545..9dd586869bee 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 ce9d1962e760..f150e0bd1679 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 a6fcb5595a3a..23cc75b6f70f 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 6d6b33e71dc0..529629ac5f77 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 1a56df276c18..20a4548fa8c0 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 c8d61161e70f..29febc6851ad 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 6248fee38657..1b4d5f430927 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 a83052ad39af..8531b4cb7b96 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 60e694ac317c..33b1a2c94560 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 5c0950d87484..419d2914950d 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 ba690d35a589..b7ece6f6ae66 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 d04fd265ff67..2a116f093c55 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 73e3673d26fe..1980ffebd1e4 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 1e1eb80246ff..2233d0aab50b 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 dbb61a274585..dd173c2fb7e8 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 9725496fd0d3..7c965d074d01 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 ad32c0dd8359..50d280dd38a3 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 324be6dfb3bb..1ce0da310081 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 a9766d01bae9..22cce8cbf1c5 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 756dc6ec7896..aa11eb36e1ba 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 9d62a966a44a..f37e347a50ba 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 53eb279e1778..18e2a92bb05f 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/query/main.nf b/modules/svdb/query/main.nf
index 61f4c8e6e2ef..292fe4ce83ff 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 ed9362b2707d..90940a5d72fb 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 e419d1532a90..3f42ad21fee3 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 c721a554677a..5f5162614687 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 87175a39abb6..17c94a34bdba 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 c5a1ca0fdefb..a5f8c6493ed0 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 08eecc01ebd9..454dfc54cea9 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 ?: "${meta.id}"
diff --git a/modules/transdecoder/longorf/main.nf b/modules/transdecoder/longorf/main.nf
index 214fd1f07430..9d5c20f2062b 100644
--- a/modules/transdecoder/longorf/main.nf
+++ b/modules/transdecoder/longorf/main.nf
@@ -18,6 +18,9 @@ process TRANSDECODER_LONGORF {
     path("${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 97b24b3fcc7b..dccc031ce164 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 ee40b780b61b..9487c7990b0c 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 742798b39ae5..0c84cfe79bd8 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 dacd72600790..969a8f73ef45 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 9ba306abab80..ef0ca088f9e1 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 1e97c83d431e..51d63de81790 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 3dd9531ec7d9..be8fad3e1d44 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 6a1847b6159a..d07e7ec1414c 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 f2dcb543940c..c86a58022382 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 ce21437dba22..1e46a6129b0f 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 fba8f054022e..22a405b9704d 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 1ccc72a9548c..4d3721b0367b 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 ?: "${meta.id}"
diff --git a/modules/untar/main.nf b/modules/untar/main.nf
index 6d1996e77d36..01205e60d008 100644
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@@ -14,6 +14,9 @@ process UNTAR {
     path "$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 294ac0b0c46b..1ce4b89b8372 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 11059a9a364b..3370ca8f3b00 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 421fc0fadb54..77275963f1b1 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 37fc51bc3aba..a01e848568b1 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 fbe646ca965b..78b95fae3f8d 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 77122c78878e..0fa5f00b592f 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 4539033dd9a4..9c993ac7cc77 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}"