diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
new file mode 100644
index 00000000..04be83db
--- /dev/null
+++ b/tests/config/pytest_modules.yml
@@ -0,0 +1,1486 @@
+abacas:
+  - modules/abacas/**
+  - tests/modules/abacas/**
+
+adapterremoval:
+  - modules/adapterremoval/**
+  - tests/modules/adapterremoval/**
+
+agrvate:
+  - modules/agrvate/**
+  - tests/modules/agrvate/**
+
+allelecounter:
+  - modules/allelecounter/**
+  - tests/modules/allelecounter/**
+
+amps:
+  - modules/amps/**
+  - tests/modules/amps/**
+
+arriba:
+  - modules/arriba/**
+  - tests/modules/arriba/**
+
+artic/guppyplex:
+  - modules/artic/guppyplex/**
+  - tests/modules/artic/guppyplex/**
+
+artic/minion:
+  - modules/artic/minion/**
+  - tests/modules/artic/minion/**
+
+assemblyscan:
+  - modules/assemblyscan/**
+  - tests/modules/assemblyscan/**
+
+ataqv/ataqv:
+  - modules/ataqv/ataqv/**
+  - tests/modules/ataqv/ataqv/**
+
+bakta:
+  - modules/bakta/**
+  - tests/modules/bakta/**
+
+bamaligncleaner:
+  - modules/bamaligncleaner/**
+  - tests/modules/bamaligncleaner/**
+
+bamtools/split:
+  - modules/bamtools/split/**
+  - tests/modules/bamtools/split/**
+
+bamutil/trimbam:
+  - modules/bamutil/trimbam/**
+  - tests/modules/bamutil/trimbam/**
+
+bandage/image:
+  - modules/bandage/image/**
+  - tests/modules/bandage/image/**
+
+bbmap/align:
+  - modules/bbmap/align/**
+  - tests/modules/bbmap/align/**
+
+bbmap/bbduk:
+  - modules/bbmap/bbduk/**
+  - tests/modules/bbmap/bbduk/**
+
+bbmap/bbsplit:
+  - modules/bbmap/bbsplit/**
+  - tests/modules/bbmap/bbsplit/**
+
+bbmap/index:
+  - modules/bbmap/index/**
+  - tests/modules/bbmap/index/**
+
+bcftools/concat:
+  - modules/bcftools/concat/**
+  - tests/modules/bcftools/concat/**
+
+bcftools/consensus:
+  - modules/bcftools/consensus/**
+  - tests/modules/bcftools/consensus/**
+
+bcftools/filter:
+  - modules/bcftools/filter/**
+  - tests/modules/bcftools/filter/**
+
+bcftools/index:
+  - modules/bcftools/index/**
+  - tests/modules/bcftools/index**
+
+bcftools/isec:
+  - modules/bcftools/isec/**
+  - tests/modules/bcftools/isec/**
+
+bcftools/merge:
+  - modules/bcftools/merge/**
+  - tests/modules/bcftools/merge/**
+
+bcftools/mpileup:
+  - modules/bcftools/mpileup/**
+  - tests/modules/bcftools/mpileup/**
+
+bcftools/norm:
+  - modules/bcftools/norm/**
+  - tests/modules/bcftools/norm/**
+
+bcftools/query:
+  - modules/bcftools/query/**
+  - tests/modules/bcftools/query/**
+
+bcftools/reheader:
+  - modules/bcftools/reheader/**
+  - tests/modules/bcftools/reheader/**
+
+bcftools/stats:
+  - modules/bcftools/stats/**
+  - tests/modules/bcftools/stats/**
+
+bcftools/view:
+  - modules/bcftools/view/**
+  - tests/modules/bcftools/view/**
+
+bedtools/bamtobed:
+  - modules/bedtools/bamtobed/**
+  - tests/modules/bedtools/bamtobed/**
+
+bedtools/complement:
+  - modules/bedtools/complement/**
+  - tests/modules/bedtools/complement/**
+
+bedtools/genomecov:
+  - modules/bedtools/genomecov/**
+  - tests/modules/bedtools/genomecov/**
+
+bedtools/getfasta:
+  - modules/bedtools/getfasta/**
+  - tests/modules/bedtools/getfasta/**
+
+bedtools/intersect:
+  - modules/bedtools/intersect/**
+  - tests/modules/bedtools/intersect/**
+
+bedtools/makewindows:
+  - modules/bedtools/makewindows/**
+  - tests/modules/bedtools/makewindows/**
+
+bedtools/maskfasta:
+  - modules/bedtools/maskfasta/**
+  - tests/modules/bedtools/maskfasta/**
+
+bedtools/merge:
+  - modules/bedtools/merge/**
+  - tests/modules/bedtools/merge/**
+
+bedtools/slop:
+  - modules/bedtools/slop/**
+  - tests/modules/bedtools/slop/**
+
+bedtools/sort:
+  - modules/bedtools/sort/**
+  - tests/modules/bedtools/sort/**
+
+bedtools/subtract:
+  - modules/bedtools/subtract/**
+  - tests/modules/bedtools/subtract/**
+
+bismark/align:
+  - modules/bismark/align/**
+  - modules/bismark/genomepreparation/**
+  - tests/modules/bismark/align/**
+
+bismark/deduplicate:
+  - modules/bismark/deduplicate/**
+  - tests/modules/bismark/deduplicate/**
+
+bismark/genomepreparation:
+  - modules/bismark/genomepreparation/**
+  - tests/modules/bismark/genomepreparation/**
+
+bismark/methylationextractor:
+  - modules/bismark/methylationextractor/**
+  - modules/bismark/genomepreparation/**
+  - tests/modules/bismark/methylationextractor/**
+
+bismark/report:
+  - modules/bismark/genomepreparation/**
+  - modules/bismark/align/**
+  - modules/bismark/deduplicate/**
+  - modules/bismark/methylationextractor/**
+  - modules/bismark/report/**
+  - tests/modules/bismark/report/**
+
+bismark/summary:
+  - modules/bismark/genomepreparation/**
+  - modules/bismark/align/**
+  - modules/bismark/deduplicate/**
+  - modules/bismark/methylationextractor/**
+  - modules/bismark/summary/**
+  - tests/modules/bismark/summary/**
+
+blast/blastn:
+  - modules/blast/blastn/**
+  - tests/modules/blast/blastn/**
+
+blast/makeblastdb:
+  - modules/blast/makeblastdb/**
+  - tests/modules/blast/makeblastdb/**
+
+bowtie/align:
+  - modules/bowtie/align/**
+  - modules/bowtie/build/**
+  - tests/modules/bowtie/align/**
+
+bowtie/build:
+  - modules/bowtie/build/**
+  - tests/modules/bowtie/build_test/**
+
+bowtie2/align:
+  - modules/bowtie2/align/**
+  - modules/bowtie2/build/**
+  - tests/modules/bowtie2/align/**
+
+bowtie2/build:
+  - modules/bowtie2/build/**
+  - tests/modules/bowtie2/build_test/**
+
+bwa/aln:
+  - modules/bwa/aln/**
+  - tests/modules/bwa/aln/**
+
+bwa/index:
+  - modules/bwa/index/**
+  - tests/modules/bwa/index/**
+
+bwa/mem:
+  - modules/bwa/mem/**
+  - tests/modules/bwa/mem/**
+
+bwa/sampe:
+  - modules/bwa/sampe/**
+  - tests/modules/bwa/sampe/**
+
+bwa/samse:
+  - modules/bwa/samse/**
+  - tests/modules/bwa/samse/**
+
+bwamem2/index:
+  - modules/bwamem2/index/**
+  - tests/modules/bwamem2/index/**
+
+bwamem2/mem:
+  - modules/bwamem2/mem/**
+  - tests/modules/bwamem2/mem/**
+
+bwameth/align:
+  - modules/bwameth/align/**
+  - tests/modules/bwameth/align/**
+
+bwameth/index:
+  - modules/bwameth/index/**
+  - tests/modules/bwameth/index/**
+
+cat/cat:
+  - modules/cat/cat/**
+  - tests/modules/cat/cat/**
+
+cat/fastq:
+  - modules/cat/fastq/**
+  - tests/modules/cat/fastq/**
+
+cellranger/count:
+  - modules/cellranger/count/**
+  - tests/modules/cellranger/count/**
+  - modules/cellranger/mkref/**
+  - tests/modules/cellranger/mkref/**
+  - modules/cellranger/gtf/**
+  - tests/modules/cellranger/gtf/**
+
+cellranger/gtf:
+  - modules/cellranger/gtf/**
+  - tests/modules/cellranger/gtf/**
+
+cellranger/mkref:
+  - modules/cellranger/mkref/**
+  - tests/modules/cellranger/mkref/**
+  - modules/cellranger/gtf/**
+  - tests/modules/cellranger/gtf/**
+
+checkm/lineagewf:
+  - modules/checkm/lineagewf/**
+  - tests/modules/checkm/lineagewf/**
+
+chromap/chromap:
+  - modules/chromap/chromap/**
+  - tests/modules/chromap/chromap/**
+
+chromap/index:
+  - modules/chromap/index/**
+  - tests/modules/chromap/index/**
+
+clonalframeml:
+  - modules/clonalframeml/**
+  - tests/modules/clonalframeml/**
+
+cmseq/polymut:
+  - modules/cmseq/polymut/**
+  - tests/modules/cmseq/polymut/**
+
+cnvkit/batch:
+  - modules/cnvkit/batch/**
+  - tests/modules/cnvkit/batch/**
+
+cooler/cload:
+  - modules/cooler/cload/**
+  - tests/modules/cooler/cload/**
+
+cooler/digest:
+  - modules/cooler/digest/**
+  - tests/modules/cooler/digest/**
+
+cooler/dump:
+  - modules/cooler/dump/**
+  - tests/modules/cooler/dump/**
+
+cooler/merge:
+  - modules/cooler/merge/**
+  - tests/modules/cooler/merge/**
+
+cooler/zoomify:
+  - modules/cooler/zoomify/**
+  - tests/software/cooler/zoomify/**
+
+csvtk/concat:
+  - modules/csvtk/concat/**
+  - tests/modules/csvtk/concat/**
+
+csvtk/split:
+  - modules/csvtk/split/**
+  - tests/modules/csvtk/split/**
+
+custom/dumpsoftwareversions:
+  - modules/custom/dumpsoftwareversions/**
+  - tests/modules/custom/dumpsoftwareversions/**
+
+custom/getchromsizes:
+  - modules/custom/getchromsizes/**
+  - tests/modules/custom/getchromsizes/**
+
+cutadapt:
+  - modules/cutadapt/**
+  - tests/modules/cutadapt/**
+
+damageprofiler:
+  - modules/damageprofiler/**
+  - tests/modules/damageprofiler/**
+
+dastool/dastool:
+  - modules/dastool/dastool/**
+  - tests/modules/dastool/dastool/**
+
+dastool/scaffolds2bin:
+  - modules/dastool/scaffolds2bin/**
+  - tests/modules/dastool/scaffolds2bin/**
+
+dedup:
+  - modules/dedup/**
+  - tests/modules/dedup/**
+
+deeptools/computematrix:
+  - modules/deeptools/computematrix/**
+  - tests/modules/deeptools/computematrix/**
+
+deeptools/plotfingerprint:
+  - modules/deeptools/plotfingerprint/**
+  - tests/modules/deeptools/plotfingerprint/**
+
+deeptools/plotheatmap:
+  - modules/deeptools/plotheatmap/**
+  - tests/modules/deeptools/plotheatmap/**
+
+deeptools/plotprofile:
+  - modules/deeptools/plotprofile/**
+  - tests/modules/deeptools/plotprofile/**
+
+delly/call:
+  - modules/delly/call/**
+  - tests/modules/delly/call/**
+
+diamond/blastp:
+  - modules/diamond/blastp/**
+  - tests/modules/diamond/blastp/**
+
+diamond/blastx:
+  - modules/diamond/blastx/**
+  - tests/modules/diamond/blastx/**
+
+diamond/makedb:
+  - modules/diamond/makedb/**
+  - tests/modules/diamond/makedb/**
+
+dragmap/align:
+  - modules/dragmap/align/**
+  - tests/modules/dragmap/align/**
+
+dragmap/hashtable:
+  - modules/dragmap/hashtable/**
+  - tests/modules/dragmap/hashtable/**
+
+dragonflye:
+  - modules/dragonflye/**
+  - tests/modules/dragonflye/**
+
+dshbio/exportsegments:
+  - modules/dshbio/exportsegments/**
+  - tests/modules/dshbio/exportsegments/**
+
+dshbio/filterbed:
+  - modules/dshbio/filterbed/**
+  - tests/modules/dshbio/filterbed/**
+
+dshbio/filtergff3:
+  - modules/dshbio/filtergff3/**
+  - tests/modules/dshbio/filtergff3/**
+
+dshbio/splitbed:
+  - modules/dshbio/splitbed/**
+  - tests/modules/dshbio/splitbed/**
+
+dshbio/splitgff3:
+  - modules/dshbio/splitgff3/**
+  - tests/modules/dshbio/splitgff3/**
+
+ectyper:
+  - modules/ectyper/**
+  - tests/modules/ectyper/**
+
+emmtyper:
+  - modules/emmtyper/**
+  - tests/modules/emmtyper/**
+
+ensemblvep:
+  - modules/ensemblvep/**
+  - tests/modules/ensemblvep/**
+
+expansionhunter:
+  - modules/expansionhunter/**
+  - tests/modules/expansionhunter/**
+
+fargene:
+  - modules/fargene/**
+  - tests/modules/fargene/**
+
+fastani:
+  - modules/fastani/**
+  - tests/modules/fastani/**
+
+fastp:
+  - modules/fastp/**
+  - tests/modules/fastp/**
+
+fastqc:
+  - modules/fastqc/**
+  - tests/modules/fastqc/**
+
+fastqscan:
+  - modules/fastqscan/**
+  - tests/modules/fastqscan/**
+
+fasttree:
+  - modules/fasttree/**
+  - tests/modules/fasttree/**
+
+fgbio/callmolecularconsensusreads:
+  - modules/fgbio/callmolecularconsensusreads/**
+  - tests/modules/fgbio/callmolecularconsensusreads/**
+
+fgbio/fastqtobam:
+  - modules/fgbio/fastqtobam/**
+  - tests/modules/fgbio/fastqtobam/**
+
+fgbio/groupreadsbyumi:
+  - modules/fgbio/groupreadsbyumi/**
+  - tests/modules/fgbio/groupreadsbyumi/**
+
+fgbio/sortbam:
+  - modules/fgbio/sortbam/**
+  - tests/modules/fgbio/sortbam/**
+
+filtlong:
+  - modules/filtlong/**
+  - tests/modules/filtlong/**
+
+flash:
+  - modules/flash/**
+  - tests/modules/flash/**
+
+freebayes:
+  - modules/freebayes/**
+  - tests/modules/freebayes/**
+
+gatk4/applybqsr:
+  - modules/gatk4/applybqsr/**
+  - tests/modules/gatk4/applybqsr/**
+
+gatk4/applyvqsr:
+  - modules/gatk4/applyvqsr/**
+  - tests/modules/gatk4/applyvqsr/**
+
+gatk4/baserecalibrator:
+  - modules/gatk4/baserecalibrator/**
+  - tests/modules/gatk4/baserecalibrator/**
+
+gatk4/bedtointervallist:
+  - modules/gatk4/bedtointervallist/**
+  - tests/modules/gatk4/bedtointervallist/**
+
+gatk4/calculatecontamination:
+  - modules/gatk4/calculatecontamination/**
+  - tests/modules/gatk4/calculatecontamination/**
+
+gatk4/createsequencedictionary:
+  - modules/gatk4/createsequencedictionary/**
+  - tests/modules/gatk4/createsequencedictionary/**
+
+gatk4/createsomaticpanelofnormals:
+  - modules/gatk4/createsomaticpanelofnormals/**
+  - tests/modules/gatk4/createsomaticpanelofnormals/**
+
+gatk4/estimatelibrarycomplexity:
+  - modules/gatk4/estimatelibrarycomplexity/**
+  - tests/modules/gatk4/estimatelibrarycomplexity/**
+
+gatk4/fastqtosam:
+  - modules/gatk4/fastqtosam/**
+  - tests/modules/gatk4/fastqtosam/**
+
+gatk4/filtermutectcalls:
+  - modules/gatk4/filtermutectcalls/**
+  - tests/modules/gatk4/filtermutectcalls/**
+
+gatk4/gatherbqsrreports:
+  - modules/gatk4/gatherbqsrreports/**
+  - tests/modules/gatk4/gatherbqsrreports/**
+
+gatk4/genomicsdbimport:
+  - modules/gatk4/genomicsdbimport/**
+  - tests/modules/gatk4/genomicsdbimport/**
+
+gatk4/genotypegvcfs:
+  - modules/gatk4/genotypegvcfs/**
+  - tests/modules/gatk4/genotypegvcfs/**
+
+gatk4/getpileupsummaries:
+  - modules/gatk4/getpileupsummaries/**
+  - tests/modules/gatk4/getpileupsummaries/**
+
+gatk4/haplotypecaller:
+  - modules/gatk4/haplotypecaller/**
+  - tests/modules/gatk4/haplotypecaller/**
+
+gatk4/indexfeaturefile:
+  - modules/gatk4/indexfeaturefile/**
+  - tests/modules/gatk4/indexfeaturefile/**
+
+gatk4/intervallisttools:
+  - modules/gatk4/intervallisttools/**
+  - tests/modules/gatk4/intervallisttools/**
+
+gatk4/learnreadorientationmodel:
+  - modules/gatk4/learnreadorientationmodel/**
+  - tests/modules/gatk4/learnreadorientationmodel/**
+
+gatk4/markduplicates:
+  - modules/gatk4/markduplicates/**
+  - tests/modules/gatk4/markduplicates/**
+
+gatk4/mergebamalignment:
+  - modules/gatk4/mergebamalignment/**
+  - tests/modules/gatk4/mergebamalignment/**
+
+gatk4/mergevcfs:
+  - modules/gatk4/mergevcfs/**
+  - tests/modules/gatk4/mergevcfs/**
+
+gatk4/mutect2:
+  - modules/gatk4/mutect2/**
+  - tests/modules/gatk4/mutect2/**
+
+gatk4/revertsam:
+  - modules/gatk4/revertsam/**
+  - tests/modules/gatk4/revertsam/**
+
+gatk4/samtofastq:
+  - modules/gatk4/samtofastq/**
+  - tests/modules/gatk4/samtofastq/**
+
+gatk4/splitncigarreads:
+  - modules/gatk4/splitncigarreads/**
+  - tests/modules/gatk4/splitncigarreads/**
+
+gatk4/variantfiltration:
+  - modules/gatk4/variantfiltration/**
+  - tests/modules/gatk4/variantfiltration/**
+
+gatk4/variantrecalibrator:
+  - modules/gatk4/variantrecalibrator/**
+  - tests/modules/gatk4/variantrecalibrator/**
+
+genmap/index:
+  - modules/genmap/index/**
+  - tests/modules/genmap/index/**
+
+genmap/mappability:
+  - modules/genmap/mappability/**
+  - tests/modules/genmap/mappability/**
+
+genrich:
+  - modules/genrich/**
+  - tests/modules/genrich/**
+
+gffread:
+  - modules/gffread/**
+  - tests/modules/gffread/**
+
+glnexus:
+  - modules/glnexus/**
+  - tests/modules/glnexus/**
+
+graphmap2/align:
+  - modules/graphmap2/align/**
+  - tests/modules/graphmap2/align/**
+
+graphmap2/index:
+  - modules/graphmap2/index/**
+  - tests/modules/graphmap2/index/**
+
+gstama/collapse:
+  - modules/gstama/collapse/**
+  - tests/modules/gstama/collapse/**
+
+gstama/merge:
+  - modules/gstama/merge/**
+  - tests/modules/gstama/merge/**
+
+gtdbtk/classifywf:
+  - modules/gtdbtk/classifywf/**
+  - tests/modules/gtdbtk/classifywf/**
+
+gubbins:
+  - modules/gubbins/**
+  - tests/modules/gubbins/**
+
+gunc/downloaddb:
+  - modules/gunc/downloaddb/**
+  - tests/modules/gunc/downloaddb/**
+
+gunc/run:
+  - modules/gunc/run/**
+  - tests/modules/gunc/run/**
+
+gunzip:
+  - modules/gunzip/**
+  - tests/modules/gunzip/**
+
+hicap:
+  - modules/hicap/**
+  - tests/modules/hicap/**
+
+hifiasm:
+  - modules/hifiasm/**
+  - tests/modules/hifiasm/**
+
+hisat2/align:
+  - modules/hisat2/align/**
+  - modules/hisat2/build/**
+  - modules/hisat2/extractsplicesites/**
+  - tests/modules/hisat2/align/**
+
+hisat2/build:
+  - modules/hisat2/build/**
+  - modules/hisat2/extractsplicesites/**
+  - tests/modules/hisat2/build_test/**
+
+hisat2/extractsplicesites:
+  - modules/hisat2/extractsplicesites/**
+  - tests/modules/hisat2/extractsplicesites/**
+
+hmmcopy/gccounter:
+  - modules/hmmcopy/gccounter/**
+  - tests/modules/hmmcopy/gccounter/**
+
+hmmcopy/generatemap:
+  - modules/hmmcopy/generatemap/**
+  - tests/modules/hmmcopy/generatemap/**
+
+hmmcopy/mapcounter:
+  - modules/hmmcopy/mapcounter/**
+  - tests/modules/hmmcopy/mapcounter/**
+
+hmmcopy/readcounter:
+  - modules/hmmcopy/readcounter/**
+  - tests/modules/hmmcopy/readcounter/**
+
+hmmer/hmmalign:
+  - modules/hmmer/hmmalign/**
+  - tests/modules/hmmer/hmmalign/**
+
+homer/annotatepeaks:
+  - modules/homer/annotatepeaks/**
+  - tests/modules/homer/annotatepeaks/**
+
+homer/findpeaks:
+  - modules/homer/findpeaks/**
+  - tests/modules/homer/findpeaks/**
+
+homer/maketagdirectory:
+  - modules/homer/maketagdirectory/**
+  - tests/modules/homer/maketagdirectory/**
+
+homer/makeucscfile:
+  - modules/homer/makeucscfile/**
+  - tests/modules/homer/makeucscfile/**
+
+idr:
+  - modules/idr/**
+  - tests/modules/idr/**
+
+imputeme/vcftoprs:
+  - modules/imputeme/vcftoprs/**
+  - tests/modules/imputeme/vcftoprs/**
+
+iqtree:
+  - modules/iqtree/**
+  - tests/modules/iqtree/**
+
+ismapper:
+  - modules/ismapper/**
+  - tests/modules/ismapper/**
+
+isoseq3/cluster:
+  - modules/isoseq3/cluster/**
+  - tests/modules/isoseq3/cluster/**
+
+isoseq3/refine:
+  - modules/isoseq3/refine/**
+  - tests/modules/isoseq3/refine/**
+
+ivar/consensus:
+  - modules/ivar/consensus/**
+  - tests/modules/ivar/consensus/**
+
+ivar/trim:
+  - modules/ivar/trim/**
+  - tests/modules/ivar/trim/**
+
+ivar/variants:
+  - modules/ivar/variants/**
+  - tests/modules/ivar/variants/**
+
+jupyternotebook:
+  - modules/jupyternotebook/**
+  - tests/modules/jupyternotebook/**
+
+kallisto/index:
+  - modules/kallisto/index/**
+  - tests/modules/kallisto/index/**
+
+kallistobustools/count:
+  - modules/kallistobustools/count/**
+  - tests/modules/kallistobustools/count/**
+
+kallistobustools/ref:
+  - modules/kallistobustools/ref/**
+  - tests/modules/kallistobustools/ref/**
+
+khmer/normalizebymedian:
+  - modules/khmer/normalizebymedian/**
+  - tests/modules/khmer/normalizebymedian/**
+
+kleborate:
+  - modules/kleborate/**
+  - tests/modules/kleborate/**
+
+kraken2/kraken2:
+  - modules/kraken2/kraken2/**
+  - modules/untar/**
+  - tests/modules/kraken2/kraken2/**
+
+krona/kronadb:
+  - modules/krona/kronadb/**
+  - tests/modules/krona/kronadb/**
+
+krona/ktimporttaxonomy:
+  - modules/krona/ktimporttaxonomy/**
+  - tests/modules/krona/ktimporttaxonomy/**
+
+last/dotplot:
+  - modules/last/dotplot/**
+  - tests/modules/last/dotplot/**
+
+last/lastal:
+  - modules/last/lastal/**
+  - tests/modules/last/lastal/**
+
+last/lastdb:
+  - modules/last/lastdb/**
+  - tests/modules/last/lastdb/**
+
+last/mafconvert:
+  - modules/last/mafconvert/**
+  - tests/modules/last/mafconvert/**
+
+last/mafswap:
+  - modules/last/mafswap/**
+  - tests/modules/last/mafswap/**
+
+last/postmask:
+  - modules/last/postmask/**
+  - tests/modules/last/postmask/**
+
+last/split:
+  - modules/last/split/**
+  - tests/modules/last/split/**
+
+last/train:
+  - modules/last/train/**
+  - tests/modules/last/train/**
+
+leehom:
+  - modules/leehom/**
+  - tests/modules/leehom/**
+
+lima:
+  - modules/lima/**
+  - tests/modules/lima/**
+
+lissero:
+  - modules/lissero/**
+  - tests/modules/lissero/**
+
+lofreq/call:
+  - modules/lofreq/call/**
+  - tests/modules/lofreq/call/**
+
+lofreq/callparallel:
+  - modules/lofreq/callparallel/**
+  - tests/modules/lofreq/callparallel/**
+
+lofreq/filter:
+  - modules/lofreq/filter/**
+  - tests/modules/lofreq/filter/**
+
+lofreq/indelqual:
+  - modules/lofreq/indelqual/**
+  - tests/modules/lofreq/indelqual/**
+
+macrel/contigs:
+  - modules/macrel/contigs/**
+  - tests/modules/macrel/contigs/**
+
+macs2/callpeak:
+  - modules/macs2/callpeak/**
+  - tests/modules/macs2/callpeak/**
+
+malt/build:
+  - modules/malt/build/**
+  - tests/modules/malt/build_test/**
+
+malt/run:
+  - modules/malt/run/**
+  - tests/modules/malt/run/**
+
+maltextract:
+  - modules/maltextract/**
+  - tests/modules/maltextract/**
+
+manta/germline:
+  - modules/manta/germline/**
+  - tests/modules/manta/germline/**
+
+manta/somatic:
+  - modules/manta/somatic/**
+  - tests/modules/manta/somatic/**
+
+manta/tumoronly:
+  - modules/manta/tumoronly/**
+  - tests/modules/manta/tumoronly/**
+
+mapdamage2:
+  - modules/mapdamage2/**
+  - tests/modules/mapdamage2/**
+
+mash/sketch:
+  - modules/mash/sketch/**
+  - tests/modules/mash/sketch/**
+
+mashtree:
+  - modules/mashtree/**
+  - tests/modules/mashtree/**
+
+maxbin2:
+  - modules/maxbin2/**
+  - tests/modules/maxbin2/**
+
+maxquant:
+  - modules/lfq/**
+  - tests/modules/maxquant/lfq/**
+
+medaka:
+  - modules/medaka/**
+  - tests/modules/medaka/**
+
+megahit:
+  - modules/megahit/**
+  - tests/modules/megahit/**
+
+meningotype:
+  - modules/meningotype/**
+  - tests/modules/meningotype/**
+
+metabat2/jgisummarizebamcontigdepths:
+  - modules/metabat2/jgisummarizebamcontigdepths/**
+  - tests/modules/metabat2/jgisummarizebamcontigdepths/**
+
+metabat2/metabat2:
+  - modules/metabat2/metabat2/**
+  - tests/modules/metabat2/metabat2/**
+
+metaphlan3:
+  - modules/metaphlan3/**
+  - tests/modules/metaphlan3/**
+
+methyldackel/extract:
+  - modules/methyldackel/extract/**
+  - tests/modules/methyldackel/extract/**
+
+methyldackel/mbias:
+  - modules/methyldackel/mbias/**
+  - tests/modules/methyldackel/mbias/**
+
+minia:
+  - modules/minia/**
+  - tests/modules/minia/**
+
+miniasm:
+  - modules/miniasm/**
+  - tests/modules/miniasm/**
+
+minimap2/align:
+  - modules/minimap2/align/**
+  - tests/modules/minimap2/align/**
+
+minimap2/index:
+  - modules/minimap2/index/**
+  - tests/modules/minimap2/index/**
+
+mlst:
+  - modules/mlst/**
+  - tests/modules/mlst/**
+
+mosdepth:
+  - modules/mosdepth/**
+  - tests/modules/mosdepth/**
+
+msisensor/msi:
+  - modules/msisensor/msi/**
+  - tests/modules/msisensor/msi/**
+
+msisensor/scan:
+  - modules/msisensor/scan/**
+  - tests/modules/msisensor/scan/**
+
+mtnucratio:
+  - modules/mtnucratio/**
+  - tests/modules/mtnucratio/**
+
+multiqc:
+  - modules/fastqc/**
+  - modules/multiqc/**
+  - tests/modules/multiqc/**
+
+mummer:
+  - modules/mummer/**
+  - tests/modules/mummer/**
+
+muscle:
+  - modules/muscle/**
+  - tests/modules/muscle/**
+
+nanolyse:
+  - modules/nanolyse/**
+  - tests/modules/nanolyse/**
+
+nanoplot:
+  - modules/nanoplot/**
+  - tests/modules/nanoplot/**
+
+ncbigenomedownload:
+  - modules/ncbigenomedownload/**
+  - tests/modules/ncbigenomedownload/**
+
+nextclade:
+  - modules/nextclade/**
+  - tests/modules/nextclade/**
+
+ngmaster:
+  - modules/ngmaster/**
+  - tests/modules/ngmaster/**
+
+nucmer:
+  - modules/nucmer/**
+  - tests/modules/nucmer/**
+
+optitype:
+  - modules/optitype/**
+  - tests/modules/optitype/**
+
+pairix:
+  - modules/pairix/**
+  - tests/modules/pairix/**
+
+pairtools/dedup:
+  - modules/pairtools/dedup/**
+  - tests/modules/pairtools/dedup/**
+
+pairtools/flip:
+  - modules/pairtools/flip/**
+  - tests/modules/pairtools/flip/**
+
+pairtools/parse:
+  - modules/pairtools/parse/**
+  - tests/modules/pairtools/parse/**
+
+pairtools/restrict:
+  - modules/pairtools/restrict/**
+  - tests/modules/pairtools/restrict/**
+
+pairtools/select:
+  - modules/pairtools/select/**
+  - tests/modules/pairtools/select/**
+
+pairtools/sort:
+  - modules/pairtools/sort/**
+  - tests/modules/pairtools/sort/**
+
+pangolin:
+  - modules/pangolin/**
+  - tests/modules/pangolin/**
+
+paraclu:
+  - modules/paraclu/**
+  - tests/modules/paraclu/**
+
+pbbam/pbmerge:
+  - modules/pbbam/pbmerge/**
+  - tests/modules/pbbam/pbmerge/**
+
+pbccs:
+  - modules/pbccs/**
+  - tests/modules/pbccs/**
+
+peddy:
+  - modules/peddy/**
+  - tests/modules/peddy/**
+
+phyloflash:
+  - modules/phyloflash/**
+  - tests/modules/phyloflash/**
+
+picard/collecthsmetrics:
+  - modules/picard/collecthsmetrics/**
+  - tests/modules/picard/collecthsmetrics/**
+
+picard/collectmultiplemetrics:
+  - modules/picard/collectmultiplemetrics/**
+  - tests/modules/picard/collectmultiplemetrics/**
+
+picard/collectwgsmetrics:
+  - modules/picard/collectwgsmetrics/**
+  - tests/modules/picard/collectwgsmetrics/**
+
+picard/filtersamreads:
+  - modules/picard/filtersamreads/**
+  - tests/modules/picard/filtersamreads/**
+
+picard/markduplicates:
+  - modules/picard/markduplicates/**
+  - tests/modules/picard/markduplicates/**
+
+picard/mergesamfiles:
+  - modules/picard/mergesamfiles/**
+  - tests/modules/picard/mergesamfiles/**
+
+picard/sortsam:
+  - modules/picard/sortsam/**
+  - tests/modules/picard/sortsam/**
+
+pirate:
+  - modules/pirate/**
+  - tests/modules/pirate/**
+
+plasmidid:
+  - modules/plasmidid/**
+  - tests/modules/plasmidid/**
+
+plink/extract:
+  - modules/plink/extract/**
+  - tests/modules/plink/extract/**
+
+plink/vcf:
+  - modules/plink/vcf/**
+  - tests/modules/plink/vcf/**
+
+plink2/vcf:
+  - modules/plink2/vcf/**
+  - tests/modules/plink2/vcf/**
+
+pmdtools/filter:
+  - modules/pmdtools/filter/**
+  - tests/modules/pmdtools/filter/**
+
+porechop:
+  - modules/porechop/**
+  - tests/modules/porechop/**
+
+preseq/lcextrap:
+  - modules/preseq/lcextrap/**
+  - tests/modules/preseq/lcextrap/**
+
+prodigal:
+  - modules/prodigal/**
+  - tests/modules/prodigal/**
+
+prokka:
+  - modules/prokka/**
+  - tests/modules/prokka/**
+
+pycoqc:
+  - modules/pycoqc/**
+  - tests/modules/pycoqc/**
+
+pydamage/analyze:
+  - modules/pydamage/analyze/**
+  - tests/modules/pydamage/analyze/**
+
+pydamage/filter:
+  - modules/pydamage/filter/**
+  - tests/modules/pydamage/filter/**
+
+qcat:
+  - modules/qcat/**
+  - tests/modules/qcat/**
+
+qualimap/bamqc:
+  - modules/qualimap/bamqc/**
+  - tests/modules/qualimap/bamqc/**
+
+quast:
+  - modules/quast/**
+  - tests/modules/quast/**
+
+racon:
+  - modules/racon/**
+  - tests/modules/racon/**
+
+rapidnj:
+  - modules/rapidnj/**
+  - tests/modules/rapidnj/**
+
+rasusa:
+  - modules/rasusa/**
+  - tests/modules/rasusa/**
+
+raxmlng:
+  - modules/raxmlng/**
+  - tests/modules/raxmlng/**
+
+rmarkdownnotebook:
+  - modules/rmarkdownnotebook/**
+  - tests/modules/rmarkdownnotebook/**
+
+roary:
+  - modules/roary/**
+  - tests/modules/roary/**
+
+rsem/calculateexpression:
+  - modules/rsem/calculateexpression/**
+  - tests/modules/rsem/calculateexpression/**
+
+rsem/preparereference:
+  - modules/rsem/preparereference/**
+  - tests/modules/rsem/preparereference/**
+
+rseqc/bamstat:
+  - modules/rseqc/bamstat/**
+  - tests/modules/rseqc/bamstat/**
+
+rseqc/inferexperiment:
+  - modules/rseqc/inferexperiment/**
+  - tests/modules/rseqc/inferexperiment/**
+
+rseqc/innerdistance:
+  - modules/rseqc/innerdistance/**
+  - tests/modules/rseqc/innerdistance/**
+
+rseqc/junctionannotation:
+  - modules/rseqc/junctionannotation/**
+  - tests/modules/rseqc/junctionannotation/**
+
+rseqc/junctionsaturation:
+  - modules/rseqc/junctionsaturation/**
+  - tests/modules/rseqc/junctionsaturation/**
+
+rseqc/readdistribution:
+  - modules/rseqc/readdistribution/**
+  - tests/modules/rseqc/readdistribution/**
+
+rseqc/readduplication:
+  - modules/rseqc/readduplication/**
+  - tests/modules/rseqc/readduplication/**
+
+rseqc/tin:
+  - modules/rseqc/tin/**
+  - tests/modules/rseqc/tin/**
+
+salmon/index:
+  - modules/salmon/index/**
+  - tests/modules/salmon/index/**
+
+salmon/quant:
+  - modules/salmon/quant/**
+  - tests/modules/salmon/quant/**
+
+samblaster:
+  - modules/samblaster/**
+  - tests/modules/samblaster/**
+
+samtools/ampliconclip:
+  - modules/samtools/ampliconclip/**
+  - tests/modules/samtools/ampliconclip/**
+
+samtools/bam2fq:
+  - modules/samtools/bam2fq/**
+  - tests/modules/samtools/bam2fq/**
+
+samtools/depth:
+  - modules/samtools/depth/**
+  - tests/modules/samtools/depth/**
+
+samtools/faidx:
+  - modules/samtools/faidx/**
+  - tests/modules/samtools/faidx/**
+
+samtools/fastq:
+  - modules/samtools/fastq/**
+  - tests/modules/samtools/fastq/**
+
+samtools/fixmate:
+  - modules/samtools/fixmate/**
+  - tests/modules/samtools/fixmate/**
+
+samtools/flagstat:
+  - modules/samtools/flagstat/**
+  - tests/modules/samtools/flagstat/**
+
+samtools/idxstats:
+  - modules/samtools/idxstats/**
+  - tests/modules/samtools/idxstats/**
+
+samtools/index:
+  - modules/samtools/index/**
+  - tests/modules/samtools/index/**
+
+samtools/merge:
+  - modules/samtools/merge/**
+  - tests/modules/samtools/merge/**
+
+samtools/mpileup:
+  - modules/samtools/mpileup/**
+  - tests/modules/samtools/mpileup/**
+
+samtools/sort:
+  - modules/samtools/sort/**
+  - tests/modules/samtools/sort/**
+
+samtools/stats:
+  - modules/samtools/stats/**
+  - tests/modules/samtools/stats/**
+
+samtools/view:
+  - modules/samtools/view/**
+  - tests/modules/samtools/view/**
+
+scoary:
+  - modules/scoary/**
+  - tests/modules/scoary/**
+
+seacr/callpeak:
+  - modules/seacr/callpeak/**
+  - tests/modules/seacr/callpeak/**
+
+seqkit/split2:
+  - modules/seqkit/split2/**
+  - tests/modules/seqkit/split2/**
+
+seqsero2:
+  - modules/seqsero2/**
+  - tests/modules/seqsero2/**
+
+seqtk/mergepe:
+  - modules/seqtk/mergepe/**
+  - tests/modules/seqtk/mergepe/**
+
+seqtk/sample:
+  - modules/seqtk/sample/**
+  - tests/modules/seqtk/sample/**
+
+seqtk/subseq:
+  - modules/seqtk/subseq/**
+  - tests/modules/seqtk/subseq/**
+
+sequenzautils/bam2seqz:
+  - modules/sequenzautils/bam2seqz/**
+  - tests/modules/sequenzautils/bam2seqz/**
+
+sequenzautils/gcwiggle:
+  - modules/sequenzautils/gcwiggle/**
+  - tests/modules/sequenzautils/gcwiggle/**
+
+seqwish/induce:
+  - modules/seqwish/induce/**
+  - tests/modules/seqwish/induce/**
+
+shovill:
+  - modules/shovill/**
+  - tests/modules/shovill/**
+
+snpdists:
+  - modules/snpdists/**
+  - tests/modules/snpdists/**
+
+snpeff:
+  - modules/snpeff/**
+  - tests/modules/snpeff/**
+
+snpsift/split:
+  - modules/snpsift/split/**
+  - tests/modules/snpsift/split/**
+
+snpsites:
+  - modules/snpsites/**
+  - tests/modules/snpsites/**
+
+spades:
+  - modules/spades/**
+  - tests/modules/spades/**
+
+spatyper:
+  - modules/spatyper/**
+  - tests/modules/spatyper/**
+
+sratools/fasterqdump:
+  - modules/sratools/fasterqdump/**
+  - tests/modules/sratools/fasterqdump/**
+
+sratools/prefetch:
+  - modules/sratools/prefetch/**
+  - tests/modules/sratools/prefetch/**
+
+staphopiasccmec:
+  - modules/staphopiasccmec/**
+  - tests/modules/staphopiasccmec/**
+
+star/align:
+  - modules/star/align/**
+  - tests/modules/star/align/**
+
+star/genomegenerate:
+  - modules/star/genomegenerate/**
+  - tests/modules/star/genomegenerate/**
+
+strelka/germline:
+  - modules/strelka/germline/**
+  - tests/modules/strelka/germline/**
+
+strelka/somatic:
+  - modules/strelka/somatic/**
+  - tests/modules/strelka/somatic/**
+
+stringtie/merge:
+  - modules/stringtie/merge/**
+  - tests/modules/stringtie/merge/**
+
+stringtie/stringtie:
+  - modules/stringtie/stringtie/**
+  - tests/modules/stringtie/stringtie/**
+
+subread/featurecounts:
+  - modules/subread/featurecounts/**
+  - tests/modules/subread/featurecounts/**
+
+tabix/bgzip:
+  - modules/tabix/bgzip/**
+  - tests/modules/tabix/bgzip/**
+
+tabix/bgziptabix:
+  - modules/tabix/bgziptabix/**
+  - tests/modules/tabix/bgziptabix/**
+
+tabix/tabix:
+  - modules/tabix/tabix/**
+  - tests/modules/tabix/tabix/**
+
+tbprofiler/profile:
+  - modules/tbprofiler/profile/**
+  - tests/modules/tbprofiler/profile/**
+
+tiddit/cov:
+  - modules/tiddit/cov/**
+  - tests/modules/tiddit/cov/**
+
+tiddit/sv:
+  - modules/tiddit/sv/**
+  - tests/modules/tiddit/sv/**
+
+trimgalore:
+  - modules/trimgalore/**
+  - tests/modules/trimgalore/**
+
+ucsc/bed12tobigbed:
+  - modules/ucsc/bed12tobigbed/**
+  - tests/modules/ucsc/bed12tobigbed/**
+
+ucsc/bedclip:
+  - modules/ucsc/bedclip/**
+  - tests/modules/ucsc/bedclip/**
+
+ucsc/bedgraphtobigwig:
+  - modules/ucsc/bedgraphtobigwig/**
+  - tests/modules/ucsc/bedgraphtobigwig/**
+
+ucsc/bigwigaverageoverbed:
+  - modules/ucsc/bigwigaverageoverbed/**
+  - tests/modules/ucsc/bigwigaverageoverbed/**
+
+ucsc/liftover:
+  - modules/ucsc/liftover/**
+  - tests/modules/ucsc/liftover/**
+
+ucsc/wigtobigwig:
+  - modules/ucsc/wigtobigwig/**
+  - tests/modules/ucsc/wigtobigwig/**
+
+ultra/pipeline:
+  - modules/ultra/pipeline/**
+  - tests/modules/ultra/pipeline/**
+
+unicycler:
+  - modules/unicycler/**
+  - tests/modules/unicycler/**
+
+untar:
+  - modules/untar/**
+  - tests/modules/untar/**
+
+unzip:
+  - modules/unzip/**
+  - tests/modules/unzip/**
+
+variantbam:
+  - modules/variantbam/**
+  - tests/modules/variantbam/**
+
+vcftools:
+  - modules/vcftools/**
+  - tests/modules/vcftools/**
+
+yara/index:
+  - modules/yara/index/**
+  - tests/modules/yara/index/**
+
+yara/mapper:
+  - modules/yara/mapper/**
+  - tests/modules/yara/mapper/**