abacas: - modules/abacas/** - tests/modules/abacas/** adapterremoval: - modules/adapterremoval/** - tests/modules/adapterremoval/** agrvate: - modules/agrvate/** - tests/modules/agrvate/** allelecounter: - modules/allelecounter/** - tests/modules/allelecounter/** arriba: - modules/arriba/** - tests/modules/arriba/** artic/guppyplex: - modules/artic/guppyplex/** - tests/modules/artic/guppyplex/** artic/minion: - modules/artic/minion/** - tests/modules/artic/minion/** bamaligncleaner: - modules/bamaligncleaner/** - tests/modules/bamaligncleaner/** 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/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/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/** chromap/chromap: - modules/chromap/chromap/** - tests/modules/chromap/chromap/** chromap/index: - modules/chromap/index/** - tests/modules/chromap/index/** cnvkit: - modules/cnvkit/** - tests/modules/cnvkit/** cooler/digest: - modules/cooler/digest/** - tests/modules/cooler/digest/** cooler/dump: - modules/cooler/dump/** - tests/modules/cooler/dump/** cutadapt: - modules/cutadapt/** - tests/modules/cutadapt/** damageprofiler: - modules/damageprofiler/** - tests/modules/damageprofiler/** 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/** 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/** ensemblvep: - modules/ensemblvep/** - tests/modules/ensemblvep/** expansionhunter: - modules/expansionhunter/** - tests/modules/expansionhunter/** fastp: - modules/fastp/** - tests/modules/fastp/** fastqc: - modules/fastqc/** - tests/modules/fastqc/** fasttree: - modules/fasttree/** - tests/modules/fasttree/** fgbio/callmolecularconsensusreads: - modules/fgbio/callmolecularconsensusreads/** - tests/modules/fgbio/callmolecularconsensusreads/** fgbio/sortbam: - modules/fgbio/sortbam/** - tests/modules/fgbio/sortbam/** flash: - modules/flash/** - tests/modules/flash/** gatk4/applybqsr: - modules/gatk4/applybqsr/** - tests/modules/gatk4/applybqsr/** gatk4/baserecalibrator: - modules/gatk4/baserecalibrator/** - tests/modules/gatk4/baserecalibrator/** gatk4/bedtointervallist: - modules/gatk4/bedtointervallist/** - tests/modules/gatk4/bedtointervallist/** gatk4/createsequencedictionary: - modules/gatk4/createsequencedictionary/** - tests/modules/gatk4/createsequencedictionary/** gatk4/fastqtosam: - modules/gatk4/fastqtosam/** - tests/modules/gatk4/fastqtosam/** gatk4/getpileupsummaries: - modules/gatk4/getpileupsummaries/** - tests/modules/gatk4/getpileupsummaries/** gatk4/haplotypecaller: - modules/gatk4/haplotypecaller/** - tests/modules/gatk4/haplotypecaller/** gatk4/intervallisttools: - modules/gatk4/intervallisttools/** - tests/modules/gatk4/intervallisttools/** 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/** genmap/index: - modules/genmap/index/** - tests/modules/genmap/index/** genmap/mappability: - modules/genmap/mappability/** - tests/modules/genmap/mappability/** gffread: - modules/gffread/** - tests/modules/gffread/** graphmap2/align: - modules/graphmap2/align/** - tests/modules/graphmap2/align/** graphmap2/index: - modules/graphmap2/index/** - tests/modules/graphmap2/index/** gubbins: - modules/gubbins/** - tests/modules/gubbins/** gunzip: - modules/gunzip/** - tests/modules/gunzip/** 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/** 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/** iqtree: - modules/iqtree/** - tests/modules/iqtree/** 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/** 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/** kraken2/kraken2: - modules/kraken2/kraken2/** - modules/untar/** - tests/modules/kraken2/kraken2/** 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/** 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/** malt/build: - modules/malt/build/** - tests/modules/malt/build_test/** malt/run: - modules/malt/run/** - tests/modules/malt/run/** mash/sketch: - modules/mash/sketch/** - tests/modules/mash/sketch/** 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/** minimap2/align: - modules/minimap2/align/** - tests/modules/minimap2/align/** minimap2/index: - modules/minimap2/index/** - tests/modules/minimap2/index/** mosdepth: - modules/mosdepth/** - tests/modules/mosdepth/** msisensor/msi: - modules/msisensor/msi/** - tests/modules/msisensor/msi/** msisensor/scan: - modules/msisensor/scan/** - tests/modules/msisensor/scan/** multiqc: - modules/fastqc/** - modules/multiqc/** - tests/modules/multiqc/** muscle: - modules/muscle/** - tests/modules/muscle/** nanolyse: - modules/nanolyse/** - tests/modules/nanolyse/** nanoplot: - modules/nanoplot/** - tests/modules/nanoplot/** nextclade: - modules/nextclade/** - tests/modules/nextclade/** 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/** pbccs: - modules/pbccs/** - tests/modules/pbccs/** 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/** plasmidid: - modules/plasmidid/** - tests/modules/plasmidid/** plink/vcf: - modules/plink/vcf/** - tests/modules/plink/vcf/** 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/** rapidnj: - modules/rapidnj/** - tests/modules/rapidnj/** rasusa: - modules/rasusa/** - tests/modules/rasusa/** raxmlng: - modules/raxmlng/** - tests/modules/raxmlng/** 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/** salmon/index: - modules/salmon/index/** - tests/modules/salmon/index/** salmon/quant: - modules/salmon/quant/** - tests/modules/salmon/quant/** samtools/ampliconclip: - modules/samtools/ampliconclip/** - tests/modules/samtools/ampliconclip/** samtools/faidx: - modules/samtools/faidx/** - tests/modules/samtools/faidx/** samtools/fastq: - modules/samtools/fastq/** - tests/modules/samtools/fastq/** 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/** seacr/callpeak: - modules/seacr/callpeak/** - tests/modules/seacr/callpeak/** seqkit/split2: - modules/seqkit/split2/** - tests/modules/seqkit/split2/** 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/** snpsites: - modules/snpsites/** - tests/modules/snpsites/** spades: - modules/spades/** - tests/modules/spades/** 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/** 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/** 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/wigtobigwig: - modules/ucsc/wigtobigwig/** - tests/modules/ucsc/wigtobigwig/** 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/**