adapterremoval:
  - software/adapterremoval/**
  - tests/software/adapterremoval/**

allelecounter:
  - software/allelecounter/**
  - tests/software/allelecounter/**

bandage_image:
  - software/bandage/image/**
  - tests/software/bandage/image/**

bcftools_consensus:
  - software/bcftools/consensus/**
  - tests/software/bcftools/consensus/**

bcftools_filter:
  - software/bcftools/filter/**
  - tests/software/bcftools/filter/**

bcftools_isec:
  - software/bcftools/isec/**
  - tests/software/bcftools/isec/**

bcftools_merge:
  - software/bcftools/merge/**
  - tests/software/bcftools/merge/**

bcftools_mpileup:
  - software/bcftools/mpileup/**
  - tests/software/bcftools/mpileup/**

bcftools_stats:
  - software/bcftools/stats/**
  - tests/software/bcftools/stats/**

bedtools_complement:
  - software/bedtools/complement/**
  - tests/software/bedtools/complement/**

bedtools_genomecov:
  - software/bedtools/genomecov/**
  - tests/software/bedtools/genomecov/**

bedtools_getfasta:
  - software/bedtools/getfasta/**
  - tests/software/bedtools/getfasta/**

bedtools_intersect:
  - software/bedtools/intersect/**
  - tests/software/bedtools/intersect/**

bedtools_maskfasta:
  - software/bedtools/maskfasta/**
  - tests/software/bedtools/maskfasta/**

bedtools_merge:
  - software/bedtools/merge/**
  - tests/software/bedtools/merge/**

bedtools_slop:
  - software/bedtools/slop/**
  - tests/software/bedtools/slop/**

bedtools_sort:
  - software/bedtools/sort/**
  - tests/software/bedtools/sort/**

bismark_align:
  - software/bismark/align/**
  - software/bismark/genomepreparation/**
  - tests/software/bismark/align/**

bismark_deduplicate:
  - software/bismark/deduplicate/**
  - tests/software/bismark/deduplicate/**

bismark_genomepreparation:
  - software/bismark/genomepreparation/**
  - tests/software/bismark/genomepreparation/**

bismark_methylationextractor:
  - software/bismark/methylationextractor/**
  - software/bismark/genomepreparation/**
  - tests/software/bismark/methylationextractor/**

bismark_report:
  - software/bismark/genomepreparation/**
  - software/bismark/align/**
  - software/bismark/deduplicate/**
  - software/bismark/methylationextractor/**
  - software/bismark/report/**
  - tests/software/bismark/report/**

bismark_summary:
  - software/bismark/genomepreparation/**
  - software/bismark/align/**
  - software/bismark/deduplicate/**
  - software/bismark/methylationextractor/**
  - software/bismark/summary/**
  - tests/software/bismark/summary/**

blast_blastn:
  - software/blast/blastn/**
  - tests/software/blast/blastn/**

blast_makeblastdb:
  - software/blast/makeblastdb/**
  - tests/software/blast/makeblastdb/**

bowtie2_align:
  - software/bowtie2/align/**
  - software/bowtie2/build/**
  - tests/software/bowtie2/align/**

bowtie2_build:
  - software/bowtie2/build/**
  - tests/software/bowtie2/build_test/**

bowtie_align:
  - software/bowtie/align/**
  - software/bowtie/build/**
  - tests/software/bowtie/align/**

bowtie_build:
  - software/bowtie/build/**
  - tests/software/bowtie/build_test/**

bwa_index:
  - software/bwa/index/**
  - tests/software/bwa/index/**

bwa_mem:
  - software/bwa/mem/**
  - tests/software/bwa/mem/**

bwamem2_index:
  - software/bwamem2/index/**
  - tests/software/bwamem2/index/**

bwamem2_mem:
  - software/bwamem2/mem/**
  - tests/software/bwamem2/mem/**

bwameth_align:
  - software/bwameth/align/**
  - tests/software/bwameth/align/**

bwameth_index:
  - software/bwameth/index/**
  - tests/software/bwameth/index/**

cat_fastq:
  - software/cat/fastq/**
  - tests/software/cat/fastq/**

cnvkit:
  - software/cnvkit/**
  - tests/software/cnvkit/**

cutadapt:
  - software/cutadapt/**
  - tests/software/cutadapt/**

dsh_filterbed:
  - software/dsh/filterbed/**
  - tests/software/dsh/filterbed/**

dsh_splitbed:
  - software/dsh/splitbed/**
  - tests/software/dsh/splitbed/**

fastp:
  - software/fastp/**
  - tests/software/fastp/**

fastqc:
  - software/fastqc/**
  - tests/software/fastqc/**

fgbio_callmolecularconsensusreads:
  - software/fgbio/callmolecularconsensusreads/**
  - tests/software/fgbio/callmolecularconsensusreads/**

fgbio_sortbam:
  - software/fgbio/sortbam/**
  - tests/software/fgbio/sortbam/**

flash:
  - software/flash/**
  - tests/software/flash/**

gatk4_applybqsr:
  - software/gatk4/applybqsr/**
  - tests/software/gatk4/applybqsr/**

gatk4_baserecalibrator:
  - software/gatk4/baserecalibrator/**
  - tests/software/gatk4/baserecalibrator/**

gatk4_bedtointervallist:
  - software/gatk4/bedtointervallist/**
  - tests/software/gatk4/bedtointervallist/**

gatk4_createsequencedictionary:
  - software/gatk4/createsequencedictionary/**
  - tests/software/gatk4/createsequencedictionary/**

gatk4_fastqtosam:
  - software/gatk4/fastqtosam/**
  - tests/software/gatk4/fastqtosam/**

gatk4_haplotypecaller:
  - software/gatk4/haplotypecaller/**
  - tests/software/gatk4/haplotypecaller/**

gatk4_markduplicates:
  - software/gatk4/markduplicates/**
  - tests/software/gatk4/markduplicates/**

gatk4_mergebamalignment:
  - software/gatk4/mergebamalignment/**
  - tests/software/gatk4/mergebamalignment/**

gatk4_mergevcfs:
  - software/gatk4/mergevcfs/**
  - tests/software/gatk4/mergevcfs/**

gatk4_revertsam:
  - software/gatk4/revertsam/**
  - tests/software/gatk4/revertsam/**

gatk4_samtofastq:
  - software/gatk4/samtofastq/**
  - tests/software/gatk4/samtofastq/**

gatk4_splitncigarreads:
  - software/gatk4/splitncigarreads/**
  - tests/software/gatk4/splitncigarreads/**

gatk4_variantfiltration:
  - software/gatk4/variantfiltration/**
  - tests/software/gatk4/variantfiltration/**

gffread:
  - software/gffread/**
  - tests/software/gffread/**

gunzip:
  - software/gunzip/**
  - tests/software/gunzip/**

hisat2_align:
  - software/hisat2/align/**
  - software/hisat2/build/**
  - software/hisat2/extractsplicesites/**
  - tests/software/hisat2/align/**

hisat2_build:
  - software/hisat2/build/**
  - software/hisat2/extractsplicesites/**
  - tests/software/hisat2/build_test/**

hisat2_extractsplicesites:
  - software/hisat2/extractsplicesites/**
  - tests/software/hisat2/extractsplicesites/**

homer_annotatepeaks:
  - software/homer/annotatepeaks/**
  - tests/software/homer/annotatepeaks/**

ivar_consensus:
  - software/ivar/consensus/**
  - tests/software/ivar/consensus/**

ivar_trim:
  - software/ivar/trim/**
  - tests/software/ivar/trim/**

ivar_variants:
  - software/ivar/variants/**
  - tests/software/ivar/variants/**

kallisto_index:
  - software/kallisto/index/**
  - tests/software/kallisto/index/**

kraken2_run:
  - software/kraken2/run/**
  - tests/software/kraken2/run/**

methyldackel_extract:
  - software/methyldackel/extract/**
  - tests/software/methyldackel/extract/**

methyldackel_mbias:
  - software/methyldackel/mbias/**
  - tests/software/methyldackel/mbias/**

minia:
  - software/minia/**
  - tests/software/minia/**

minimap2_align:
  - software/minimap2/align/**
  - tests/software/minimap2/align/**

mosdepth:
  - software/mosdepth/**
  - tests/software/mosdepth/**

msisensor_msi:
  - software/msisensor/msi/**
  - tests/software/msisensor/msi/**

msisensor_scan:
  - software/msisensor/scan/**
  - tests/software/msisensor/scan/**

multiqc:
  - software/fastqc/**
  - software/multiqc/**
  - tests/software/multiqc/**

optitype:
  - software/optitype/**
  - tests/software/optitype/**

pangolin:
  - software/pangolin/**
  - tests/software/pangolin/**

picard_collectmultiplemetrics:
  - software/picard/collectmultiplemetrics/**
  - tests/software/picard/collectmultiplemetrics/**

picard_collectwgsmetrics:
  - software/picard/collectwgsmetrics/**
  - tests/software/picard/collectwgsmetrics/**

picard_markduplicates:
  - software/picard/markduplicates/**
  - tests/software/picard/markduplicates/**

picard_mergesamfiles:
  - software/picard/mergesamfiles/**
  - tests/software/picard/mergesamfiles/**

preseq_lcextrap:
  - software/preseq/lcextrap/**
  - tests/software/preseq/lcextrap/**

prodigal:
  - software/prodigal/**
  - tests/software/prodigal/**

prokka:
  - software/prokka/**
  - tests/software/prokka/**

qualimap_bamqc:
  - software/qualimap/bamqc/**
  - tests/software/qualimap/bamqc/**

quast:
  - software/quast/**
  - tests/software/quast/**

salmon_index:
  - software/salmon/index/**
  - tests/software/salmon/index/**

salmon_quant:
  - software/salmon/quant/**
  - tests/software/salmon/quant/**

samtools_faidx:
  - software/samtools/faidx/**
  - tests/software/samtools/faidx/**

samtools_fastq:
  - software/samtools/fastq/**
  - tests/software/samtools/fastq/**

samtools_flagstat:
  - software/samtools/flagstat/**
  - tests/software/samtools/flagstat/**

samtools_idxstats:
  - software/samtools/idxstats/**
  - tests/software/samtools/idxstats/**

samtools_index:
  - software/samtools/index/**
  - tests/software/samtools/index/**

samtools_merge:
  - software/samtools/merge/**
  - tests/software/samtools/merge/**

samtools_mpileup:
  - software/samtools/mpileup/**
  - tests/software/samtools/mpileup/**

samtools_sort:
  - software/samtools/sort/**
  - tests/software/samtools/sort/**

samtools_stats:
  - software/samtools/stats/**
  - tests/software/samtools/stats/**

samtools_view:
  - software/samtools/view/**
  - tests/software/samtools/view/**

seacr_callpeak:
  - software/seacr/callpeak/**
  - tests/software/seacr/callpeak/**

seqkit_split2:
  - software/seqkit/split2/**
  - tests/software/seqkit/split2/**

sequenza_bam2seqz:
  - software/sequenza/bam2seqz/**
  - tests/software/sequenza/bam2seqz/**

sequenza_wiggle:
  - software/sequenza/wiggle/**
  - tests/software/sequenza/wiggle/**

sequenzautils_bam2seqz:
  - software/sequenzautils/bam2seqz/**
  - tests/software/sequenzautils/bam2seqz/**

sequenzautils_gcwiggle:
  - software/sequenzautils/gcwiggle/**
  - tests/software/sequenzautils/gcwiggle/**

seqwish_induce:
  - software/seqwish/induce/**
  - tests/software/seqwish/induce/**

shovill:
  - software/shovill/**
  - tests/software/shovill/**

spades:
  - software/spades/**
  - tests/software/spades/**

star_align:
  - software/star/align/**
  - tests/software/star/align/**

star_genomegenerate:
  - software/star/genomegenerate/**
  - tests/software/star/genomegenerate/**

strelka_germline:
  - software/strelka/germline/**
  - tests/software/strelka/germline/**

stringtie:
  - software/stringtie/**
  - tests/software/stringtie/**

subread_featurecounts:
  - software/subread/featurecounts/**
  - tests/software/subread/featurecounts/**

tabix_bgzip:
  - software/tabix/bgzip/**
  - tests/software/tabix/bgzip/**

tabix_tabix:
  - software/tabix/tabix/**
  - tests/software/tabix/tabix/**

tiddit_sv:
  - software/tiddit/sv/**
  - tests/software/tiddit/sv/**

trimgalore:
  - software/trimgalore/**
  - tests/software/trimgalore/**

ucsc_bed12tobigbed:
  - software/ucsc/bed12tobigbed/**
  - tests/software/ucsc/bed12tobigbed/**

ucsc_bedgraphtobigwig:
  - software/ucsc/bedgraphtobigwig/**
  - tests/software/ucsc/bedgraphtobigwig/**

unicycler:
  - software/unicycler/**
  - tests/software/unicycler/**

untar:
  - software/untar/**
  - tests/software/untar/**

vcftools:
  - software/vcftools/**
  - tests/software/vcftools/**

yara:
  - software/yara/mapper/**
  - tests/software/yara/mapper/**

yara_index:
  - software/yara/index/**
  - tests/software/yara/index/**