abacas: - modules/abacas/** - tests/modules/abacas/** abricate/run: - modules/abricate/run/** - tests/modules/abricate/run/** abricate/summary: - modules/abricate/summary/** - tests/modules/abricate/summary/** adapterremoval: - modules/adapterremoval/** - tests/modules/adapterremoval/** adapterremovalfixprefix: - modules/adapterremovalfixprefix/** - tests/modules/adapterremovalfixprefix/** agrvate: - modules/agrvate/** - tests/modules/agrvate/** allelecounter: - modules/allelecounter/** - tests/modules/allelecounter/** amplify/predict: - modules/amplify/predict/** - tests/modules/amplify/predict/** amps: - modules/amps/** - tests/modules/amps/** amrfinderplus/run: - modules/amrfinderplus/run/** - tests/modules/amrfinderplus/run/** amrfinderplus/update: - modules/amrfinderplus/update/** - tests/modules/amrfinderplus/update/** antismash/antismashlitedownloaddatabases: - modules/antismash/antismashlitedownloaddatabases/** - tests/modules/antismash/antismashlitedownloaddatabases/** arriba: - modules/arriba/** - tests/modules/arriba/** artic/guppyplex: - modules/artic/guppyplex/** - tests/modules/artic/guppyplex/** artic/minion: - modules/artic/minion/** - tests/modules/artic/minion/** ascat: - modules/ascat/** - tests/modules/ascat/** 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/** bamcmp: - modules/bamcmp/** - tests/modules/bamcmp/** bamtools/convert: - modules/bamtools/convert/** - tests/modules/bamtools/convert/** 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/** bbmap/pileup: - modules/bbmap/pileup/** - tests/modules/bbmap/pileup/** bcftools/annotate: - modules/bcftools/annotate/** - tests/modules/bcftools/annotate/** 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/sort: - modules/bcftools/sort/** - tests/modules/bcftools/sort/** bcftools/stats: - modules/bcftools/stats/** - tests/modules/bcftools/stats/** bcftools/view: - modules/bcftools/view/** - tests/modules/bcftools/view/** bclconvert: - modules/bclconvert/** - tests/modules/bclconvert/** 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/** biobambam/bammarkduplicates2: - modules/biobambam/bammarkduplicates2/** - tests/modules/biobambam/bammarkduplicates2/** biobambam/bamsormadup: - modules/biobambam/bamsormadup/** - tests/modules/biobambam/bamsormadup/** biscuit/align: - modules/biscuit/index/** - modules/biscuit/align/** - tests/modules/biscuit/align/** biscuit/biscuitblaster: - modules/biscuit/index/** - modules/biscuit/biscuitblaster/** - tests/modules/biscuit/biscuitblaster/** biscuit/bsconv: - modules/biscuit/index/** - modules/biscuit/bsconv/** - tests/modules/biscuit/bsconv/** biscuit/epiread: - modules/biscuit/index/** - modules/biscuit/epiread/** - tests/modules/biscuit/epiread/** biscuit/index: - modules/biscuit/index/** - tests/modules/biscuit/index/** biscuit/mergecg: - modules/biscuit/index/** - modules/biscuit/mergecg/** - tests/modules/biscuit/mergecg/** biscuit/pileup: - modules/biscuit/index/** - modules/biscuit/pileup/** - tests/modules/biscuit/pileup/** biscuit/qc: - modules/biscuit/index/** - modules/biscuit/qc/** - tests/modules/biscuit/qc/** biscuit/vcf2bed: - modules/biscuit/vcf2bed/** - tests/modules/biscuit/vcf2bed/** 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/** bracken/bracken: - modules/bracken/bracken/** - tests/modules/bracken/bracken/** busco: - modules/busco/** - tests/modules/busco/** 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/mkfastq: - modules/cellranger/mkfastq/** - tests/modules/cellranger/mkfastq/** cellranger/mkgtf: - modules/cellranger/mkgtf/** - tests/modules/cellranger/mkgtf/** cellranger/mkref: - modules/cellranger/mkref/** - tests/modules/cellranger/mkref/** - modules/cellranger/gtf/** - tests/modules/cellranger/gtf/** centrifuge/centrifuge: - modules/centrifuge/centrifuge/** - tests/modules/centrifuge/centrifuge/** 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/** controlfreec/assesssignificance: - modules/controlfreec/assesssignificance/** - tests/modules/controlfreec/assesssignificance/** controlfreec/freec: - modules/controlfreec/freec/** - tests/modules/controlfreec/freec/** controlfreec/freec2bed: - modules/controlfreec/freec2bed/** - tests/modules/controlfreec/freec2bed/** controlfreec/freec2circos: - modules/controlfreec/freec2circos/** - tests/modules/controlfreec/freec2circos/** controlfreec/makegraph: - modules/controlfreec/makegraph/** - tests/modules/controlfreec/makegraph/** 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/fastatocontig2bin: - modules/dastool/fastatocontig2bin/** - tests/modules/dastool/fastatocontig2bin/** dastool/scaffolds2bin: - modules/dastool/scaffolds2bin/** - tests/modules/dastool/scaffolds2bin/** dedup: - modules/dedup/** - tests/modules/dedup/** deeparg/downloaddata: - modules/deeparg/downloaddata/** - tests/modules/deeparg/downloaddata/** deeparg/predict: - modules/deeparg/predict/** - tests/modules/deeparg/predict/** deeptools/bamcoverage: - modules/deeptools/bamcoverage/** - tests/modules/deeptools/bamcoverage/** 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/** deepvariant: - modules/deepvariant/** - tests/modules/deepvariant/** 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/** elprep/filter: - modules/elprep/filter/** - tests/modules/elprep/filter/** elprep/merge: - modules/elprep/merge/** - tests/modules/elprep/merge/** elprep/split: - modules/elprep/split/** - tests/modules/elprep/split/** emmtyper: - modules/emmtyper/** - tests/modules/emmtyper/** ensemblvep: - modules/ensemblvep/** - tests/modules/ensemblvep/** expansionhunter: - modules/expansionhunter/** - tests/modules/expansionhunter/** faqcs: - modules/faqcs/** - tests/modules/faqcs/** 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/** gamma: - modules/gamma/** - tests/modules/gamma/** gatk4/applybqsr: - modules/gatk4/applybqsr/** - tests/modules/gatk4/applybqsr/** gatk4/applybqsrspark: - modules/gatk4/applybqsrspark/** - tests/modules/gatk4/applybqsrspark/** gatk4/applyvqsr: - modules/gatk4/applyvqsr/** - tests/modules/gatk4/applyvqsr/** gatk4/baserecalibrator: - modules/gatk4/baserecalibrator/** - tests/modules/gatk4/baserecalibrator/** gatk4/baserecalibratorspark: - modules/gatk4/baserecalibratorspark/** - tests/modules/gatk4/baserecalibratorspark/** gatk4/bedtointervallist: - modules/gatk4/bedtointervallist/** - tests/modules/gatk4/bedtointervallist/** gatk4/calculatecontamination: - modules/gatk4/calculatecontamination/** - tests/modules/gatk4/calculatecontamination/** gatk4/combinegvcfs: - modules/gatk4/combinegvcfs/** - tests/modules/gatk4/combinegvcfs/** 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/gatherpileupsummaries: - modules/gatk4/gatherpileupsummaries/** - tests/modules/gatk4/gatherpileupsummaries/** 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/intervallisttobed: - modules/gatk4/intervallisttobed/** - tests/modules/gatk4/intervallisttobed/** 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/markduplicatesspark: - modules/gatk4/markduplicatesspark/** - tests/modules/gatk4/markduplicatesspark/** gatk4/mergebamalignment: - modules/gatk4/mergebamalignment/** - tests/modules/gatk4/mergebamalignment/** gatk4/mergemutectstats: - modules/gatk4/mergemutectstats/** - tests/modules/gatk4/mergemutectstats/** 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/selectvariants: - modules/gatk4/selectvariants/** - tests/modules/gatk4/selectvariants/** 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/** gstama/polyacleanup: - modules/gstama/polyacleanup/** - tests/modules/gstama/polyacleanup/** 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/** hamronization/deeparg: - modules/hamronization/deeparg/** - tests/modules/hamronization/deeparg/** hamronization/summarize: - modules/hamronization/summarize/** - tests/modules/hamronization/summarize/** happy/happy: - modules/happy/happy/** - tests/modules/happy/happy/** happy/prepy: - modules/happy/prepy/** - tests/modules/happy/prepy/** 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/** hmmer/hmmsearch: - modules/hmmer/hmmsearch/** - tests/modules/hmmer/hmmsearch/** homer/annotatepeaks: - modules/homer/annotatepeaks/** - tests/modules/homer/annotatepeaks/** homer/findpeaks: - modules/homer/findpeaks/** - modules/homer/maketagdirectory/** - tests/modules/homer/findpeaks/** homer/maketagdirectory: - modules/homer/maketagdirectory/** - tests/modules/homer/maketagdirectory/** homer/makeucscfile: - modules/homer/makeucscfile/** - tests/modules/homer/makeucscfile/** homer/pos2bed: - modules/homer/pos2bed/** - modules/homer/maketagdirectory/** - modules/homer/findpeaks/** - tests/modules/homer/pos2bed/** hpsuissero: - modules/hpsuissero/** - tests/modules/hpsuissero/** ichorcna/createpon: - modules/ichorcna/createpon/** - tests/modules/ichorcna/createpon/** ichorcna/run: - modules/ichorcna/run/** - tests/modules/ichorcna/run/** 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/** kaiju/kaiju: - modules/kaiju/kaiju/** - tests/modules/kaiju/kaiju/** kaiju/kaiju2table: - modules/kaiju/kaiju2table/** - tests/modules/kaiju/kaiju2table/** 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/** krona/ktimporttext: - modules/krona/ktimporttext/** - tests/modules/krona/ktimporttext/** krona/ktupdatetaxonomy: - modules/krona/ktupdatetaxonomy/** - tests/modules/krona/ktupdatetaxonomy/** 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/** legsta: - modules/legsta/** - tests/modules/legsta/** 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: - 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modules/picard/collectmultiplemetrics/** - tests/modules/picard/collectmultiplemetrics/** picard/collectwgsmetrics: - modules/picard/collectwgsmetrics/** - tests/modules/picard/collectwgsmetrics/** picard/createsequencedictionary: - modules/picard/createsequencedictionary/** - tests/modules/picard/createsequencedictionary/** picard/crosscheckfingerprints: - modules/picard/crosscheckfingerprints/** - tests/modules/picard/crosscheckfingerprints/** picard/filtersamreads: - modules/picard/filtersamreads/** - tests/modules/picard/filtersamreads/** picard/fixmateinformation: - modules/picard/fixmateinformation/** - tests/modules/picard/fixmateinformation/** picard/liftovervcf: - modules/picard/liftovervcf/** - tests/modules/picard/liftovervcf/** 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/** picard/sortvcf: - modules/picard/sortvcf/** - tests/modules/picard/sortvcf/** 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/extract: - modules/plink2/extract/** - tests/modules/plink2/extract/** plink2/score: - modules/plink2/score/** - tests/modules/plink2/score/** 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/ccurve: - modules/preseq/ccurve/** - tests/modules/preseq/ccurve/** preseq/lcextrap: - modules/preseq/lcextrap/** - tests/modules/preseq/lcextrap/** prinseqplusplus: - modules/prinseqplusplus/** - tests/modules/prinseqplusplus/** 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/** qualimap/bamqccram: - modules/qualimap/bamqccram/** - tests/modules/qualimap/bamqccram/** quast: - modules/quast/** - tests/modules/quast/** racon: - modules/racon/** - tests/modules/racon/** rapidnj: - modules/rapidnj/** - tests/modules/rapidnj/** rasusa: - modules/rasusa/** - tests/modules/rasusa/** raven: - modules/raven/** - tests/modules/raven/** raxmlng: - modules/raxmlng/** - tests/modules/raxmlng/** rgi/main: - modules/rgi/main/** - tests/modules/rgi/main/** 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/** - 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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/pair: - modules/seqkit/pair/** - tests/modules/seqkit/pair/** seqkit/replace: - modules/seqkit/replace/** - tests/modules/seqkit/replace/** seqkit/split2: - modules/seqkit/split2/** - tests/modules/seqkit/split2/** seqkit/stats: - modules/seqkit/stats/** - tests/modules/seqkit/stats/** seqsero2: - modules/seqsero2/** - tests/modules/seqsero2/** seqtk/mergepe: - modules/seqtk/mergepe/** - tests/modules/seqtk/mergepe/** seqtk/rename: - modules/seqtk/rename/** - tests/modules/seqtk/rename/** seqtk/sample: - modules/seqtk/sample/** - tests/modules/seqtk/sample/** seqtk/seq: - modules/seqtk/seq/** - tests/modules/seqtk/seq/** 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/** shasum: - modules/shasum/** - tests/modules/shasum/** shigatyper: - modules/shigatyper/** - tests/modules/shigatyper/** shovill: - modules/shovill/** - tests/modules/shovill/** sistr: - modules/sistr/** - tests/modules/sistr/** slimfastq: - modules/slimfastq/** - tests/modules/slimfastq/** snapaligner/index: - modules/snapaligner/index/** - tests/modules/snapaligner/index/** snapaligner/paired: - modules/snapaligner/paired/** - tests/modules/snapaligner/paired/** snapaligner/single: - modules/snapaligner/single/** - tests/modules/snapaligner/single/** 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/** sourmash/sketch: - modules/sourmash/sketch/** - tests/modules/sourmash/sketch/** 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/** srst2/srst2: - modules/srst2/srst2/** - tests/modules/srst2/srst2/** ssuissero: - modules/ssuissero/** - tests/modules/ssuissero/** stadeniolib/scramble: - modules/stadeniolib/scramble/** - tests/modules/stadeniolib/scramble/** staphopiasccmec: - modules/staphopiasccmec/** - tests/modules/staphopiasccmec/** star/align: - modules/star/align/** - tests/modules/star/align/** star/genomegenerate: - modules/star/genomegenerate/** - tests/modules/star/genomegenerate/** stranger: - modules/stranger/** - tests/modules/stranger/** 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/** svdb/merge: - modules/svdb/merge/** - tests/modules/svdb/merge/** svdb/query: - modules/svdb/query/** - tests/modules/svdb/query/** 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/** test/template: - modules/test/template/** - tests/modules/test/template/** tiddit/cov: - modules/tiddit/cov/** - tests/modules/tiddit/cov/** tiddit/sv: - modules/tiddit/sv/** - tests/modules/tiddit/sv/** transdecoder/longorf: - modules/transdecoder/longorf/** - tests/modules/transdecoder/longorf/** transdecoder/predict: - modules/transdecoder/predict/** - tests/modules/transdecoder/predict/** 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/** umitools/dedup: - modules/umitools/dedup/** - modules/umitools/extract/** - tests/modules/umitools/dedup/** umitools/extract: - modules/umitools/extract/** - tests/modules/umitools/extract/** unicycler: - modules/unicycler/** - tests/modules/unicycler/** untar: - modules/untar/** - tests/modules/untar/** unzip: - modules/unzip/** - tests/modules/unzip/** vardictjava: - modules/vardictjava/** - tests/modules/vardictjava/** variantbam: - modules/variantbam/** - tests/modules/variantbam/** vcfanno: - modules/vcfanno/** - tests/modules/vcfanno/** vcflib/vcfuniq: - modules/vcflib/vcfuniq/** - tests/modules/vcflib/vcfuniq/** vcftools: - modules/vcftools/** - tests/modules/vcftools/** yara/index: - modules/yara/index/** - tests/modules/yara/index/** yara/mapper: - modules/yara/mapper/** - tests/modules/yara/mapper/**