mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
989fb7d5b7
* new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem * Module samtools/fastq: * output compressed fastq.gz file(s) * add if conditionals for single/paired reads * samtools/fastq: modified test.yml * samtools/fastq: modified main.nf to avoid duplicated part of the script section * fix README.md * modify test path gatk4 * fix config * Add new module gatk4/haplotypecaller * solve check issues * fix test.yml file * fix test.yml gz.tbi * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: suzannejin <suzanne.jin@crg.eu> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
495 lines
10 KiB
YAML
Executable file
495 lines
10 KiB
YAML
Executable file
adapterremoval:
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- software/adapterremoval/**
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- tests/software/adapterremoval/**
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allelecounter:
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- software/allelecounter/**
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- tests/software/allelecounter/**
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bandage_image:
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- software/bandage/image/**
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- tests/software/bandage/image/**
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bcftools_consensus:
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- software/bcftools/consensus/**
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- tests/software/bcftools/consensus/**
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bcftools_filter:
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- software/bcftools/filter/**
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- tests/software/bcftools/filter/**
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bcftools_isec:
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- software/bcftools/isec/**
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- tests/software/bcftools/isec/**
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bcftools_merge:
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- software/bcftools/merge/**
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- tests/software/bcftools/merge/**
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bcftools_mpileup:
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- software/bcftools/mpileup/**
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- tests/software/bcftools/mpileup/**
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bcftools_stats:
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- software/bcftools/stats/**
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- tests/software/bcftools/stats/**
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bedtools_complement:
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- software/bedtools/complement/**
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- tests/software/bedtools/complement/**
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bedtools_genomecov:
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- software/bedtools/genomecov/**
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- tests/software/bedtools/genomecov/**
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bedtools_getfasta:
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- software/bedtools/getfasta/**
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- tests/software/bedtools/getfasta/**
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bedtools_intersect:
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- software/bedtools/intersect/**
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- tests/software/bedtools/intersect/**
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bedtools_maskfasta:
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- software/bedtools/maskfasta/**
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- tests/software/bedtools/maskfasta/**
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bedtools_merge:
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- software/bedtools/merge/**
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- tests/software/bedtools/merge/**
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bedtools_slop:
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- software/bedtools/slop/**
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- tests/software/bedtools/slop/**
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bedtools_sort:
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- software/bedtools/sort/**
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- tests/software/bedtools/sort/**
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bismark_align:
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- software/bismark/align/**
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- software/bismark/genomepreparation/**
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- tests/software/bismark/align/**
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bismark_deduplicate:
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- software/bismark/deduplicate/**
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- tests/software/bismark/deduplicate/**
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bismark_genomepreparation:
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- software/bismark/genomepreparation/**
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- tests/software/bismark/genomepreparation/**
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bismark_methylationextractor:
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- software/bismark/methylationextractor/**
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- software/bismark/genomepreparation/**
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- tests/software/bismark/methylationextractor/**
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bismark_report:
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- software/bismark/genomepreparation/**
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- software/bismark/align/**
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- software/bismark/deduplicate/**
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- software/bismark/methylationextractor/**
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- software/bismark/report/**
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- tests/software/bismark/report/**
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bismark_summary:
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- software/bismark/genomepreparation/**
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- software/bismark/align/**
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- software/bismark/deduplicate/**
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- software/bismark/methylationextractor/**
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- software/bismark/summary/**
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- tests/software/bismark/summary/**
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blast_blastn:
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- software/blast/blastn/**
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- tests/software/blast/blastn/**
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blast_makeblastdb:
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- software/blast/makeblastdb/**
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- tests/software/blast/makeblastdb/**
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bowtie2_align:
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- software/bowtie2/align/**
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- software/bowtie2/build/**
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- tests/software/bowtie2/align/**
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bowtie2_build:
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- software/bowtie2/build/**
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- tests/software/bowtie2/build_test/**
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bowtie_align:
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- software/bowtie/align/**
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- software/bowtie/build/**
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- tests/software/bowtie/align/**
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bowtie_build:
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- software/bowtie/build/**
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- tests/software/bowtie/build_test/**
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bwa_index:
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- software/bwa/index/**
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- tests/software/bwa/index/**
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bwa_mem:
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- software/bwa/mem/**
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- tests/software/bwa/mem/**
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bwamem2_index:
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- software/bwamem2/index/**
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- tests/software/bwamem2/index/**
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bwamem2_mem:
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- software/bwamem2/mem/**
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- tests/software/bwamem2/mem/**
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bwameth_align:
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- software/bwameth/align/**
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- tests/software/bwameth/align/**
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bwameth_index:
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- software/bwameth/index/**
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- tests/software/bwameth/index/**
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cat_fastq:
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- software/cat/fastq/**
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- tests/software/cat/fastq/**
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cnvkit:
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- software/cnvkit/**
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- tests/software/cnvkit/**
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cutadapt:
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- software/cutadapt/**
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- tests/software/cutadapt/**
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dsh_filterbed:
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- software/dsh/filterbed/**
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- tests/software/dsh/filterbed/**
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dsh_splitbed:
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- software/dsh/splitbed/**
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- tests/software/dsh/splitbed/**
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fastp:
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- software/fastp/**
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- tests/software/fastp/**
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fastqc:
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- software/fastqc/**
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- tests/software/fastqc/**
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flash:
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- software/flash/**
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- tests/software/flash/**
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gatk4_applybqsr:
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- software/gatk4/applybqsr/**
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- tests/software/gatk4/applybqsr/**
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gatk4_baserecalibrator:
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- software/gatk4/baserecalibrator/**
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- tests/software/gatk4/baserecalibrator/**
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gatk4_bedtointervallist:
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- software/gatk4/bedtointervallist/**
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- tests/software/gatk4/bedtointervallist/**
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gatk4_createsequencedictionary:
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- software/gatk4/createsequencedictionary/**
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- tests/software/gatk4/createsequencedictionary/**
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gatk4_fastqtosam:
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- software/gatk4/fastqtosam/**
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- tests/software/gatk4/fastqtosam/**
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gatk4_haplotypecaller:
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- software/gatk4/haplotypecaller/**
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- tests/software/gatk4/haplotypecaller/**
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gatk4_mergebamalignment:
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- software/gatk4/mergebamalignment/**
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- tests/software/gatk4/mergebamalignment/**
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gatk4_mergevcfs:
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- software/gatk4/mergevcfs/**
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- tests/software/gatk4/mergevcfs/**
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gatk4_revertsam:
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- software/gatk4/revertsam/**
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- tests/software/gatk4/revertsam/**
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gatk4_samtofastq:
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- software/gatk4/samtofastq/**
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- tests/software/gatk4/samtofastq/**
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gatk4_splitncigarreads:
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- software/gatk4/splitncigarreads/**
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- tests/software/gatk4/splitncigarreads/**
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gatk4_variantfiltration:
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- software/gatk4/variantfiltration/**
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- tests/software/gatk4/variantfiltration/**
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gffread:
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- software/gffread/**
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- tests/software/gffread/**
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gunzip:
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- software/gunzip/**
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- tests/software/gunzip/**
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hisat2_align:
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- software/hisat2/align/**
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- software/hisat2/build/**
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/align/**
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hisat2_build:
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- software/hisat2/build/**
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/build_test/**
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hisat2_extractsplicesites:
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/extractsplicesites/**
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homer_annotatepeaks:
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- software/homer/annotatepeaks/**
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- tests/software/homer/annotatepeaks/**
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ivar_consensus:
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- software/ivar/consensus/**
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- tests/software/ivar/consensus/**
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ivar_trim:
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- software/ivar/trim/**
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- tests/software/ivar/trim/**
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ivar_variants:
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- software/ivar/variants/**
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- tests/software/ivar/variants/**
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kallisto_index:
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- software/kallisto/index/**
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- tests/software/kallisto/index/**
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kraken2_run:
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- software/kraken2/run/**
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- tests/software/kraken2/run/**
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methyldackel_extract:
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- software/methyldackel/extract/**
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- tests/software/methyldackel/extract/**
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methyldackel_mbias:
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- software/methyldackel/mbias/**
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- tests/software/methyldackel/mbias/**
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minia:
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- software/minia/**
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- tests/software/minia/**
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minimap2_align:
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- software/minimap2/align/**
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- tests/software/minimap2/align/**
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mosdepth:
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- software/mosdepth/**
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- tests/software/mosdepth/**
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msisensor_scan:
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- software/msisensor/scan/**
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- tests/software/msisensor/scan/**
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msisensor_msi:
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- software/msisensor/msi/**
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- tests/software/msisensor/msi/**
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multiqc:
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- software/fastqc/**
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- software/multiqc/**
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- tests/software/multiqc/**
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optitype:
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- software/optitype/**
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- tests/software/optitype/**
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pangolin:
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- software/pangolin/**
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- tests/software/pangolin/**
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picard_collectmultiplemetrics:
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- software/picard/collectmultiplemetrics/**
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- tests/software/picard/collectmultiplemetrics/**
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picard_collectwgsmetrics:
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- software/picard/collectwgsmetrics/**
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- tests/software/picard/collectwgsmetrics/**
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picard_markduplicates:
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- software/picard/markduplicates/**
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- tests/software/picard/markduplicates/**
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picard_mergesamfiles:
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- software/picard/mergesamfiles/**
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- tests/software/picard/mergesamfiles/**
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preseq_lcextrap:
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- software/preseq/lcextrap/**
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- tests/software/preseq/lcextrap/**
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prodigal:
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- software/prodigal/**
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- tests/software/prodigal/**
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prokka:
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- software/prokka/**
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- tests/software/prokka/**
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qualimap_bamqc:
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- software/qualimap/bamqc/**
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- tests/software/qualimap/bamqc/**
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quast:
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- software/quast/**
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- tests/software/quast/**
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salmon_index:
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- software/salmon/index/**
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- tests/software/salmon/index/**
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salmon_quant:
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- software/salmon/quant/**
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- tests/software/salmon/quant/**
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samtools_faidx:
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- software/samtools/faidx/**
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- tests/software/samtools/faidx/**
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samtools_fastq:
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- software/samtools/fastq/**
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- tests/software/samtools/fastq/**
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samtools_flagstat:
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- software/samtools/flagstat/**
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- tests/software/samtools/flagstat/**
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samtools_idxstats:
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- software/samtools/idxstats/**
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- tests/software/samtools/idxstats/**
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samtools_index:
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- software/samtools/index/**
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- tests/software/samtools/index/**
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samtools_merge:
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- software/samtools/merge/**
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- tests/software/samtools/merge/**
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samtools_mpileup:
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- software/samtools/mpileup/**
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- tests/software/samtools/mpileup/**
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samtools_sort:
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- software/samtools/sort/**
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- tests/software/samtools/sort/**
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samtools_stats:
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- software/samtools/stats/**
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- tests/software/samtools/stats/**
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samtools_view:
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- software/samtools/view/**
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- tests/software/samtools/view/**
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seacr_callpeak:
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- software/seacr/callpeak/**
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- tests/software/seacr/callpeak/**
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seqkit_split2:
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- software/seqkit/split2/**
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- tests/software/seqkit/split2/**
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sequenza_bam2seqz:
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- software/sequenza/bam2seqz/**
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- tests/software/sequenza/bam2seqz/**
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sequenza_wiggle:
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- software/sequenza/wiggle/**
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- tests/software/sequenza/wiggle/**
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sequenzautils_gcwiggle:
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- software/sequenzautils/gcwiggle/**
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- tests/software/sequenzautils/gcwiggle/**
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seqwish_induce:
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- software/seqwish/induce/**
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- tests/software/seqwish/induce/**
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shovill:
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- software/shovill/**
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- tests/software/shovill/**
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spades:
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- software/spades/**
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- tests/software/spades/**
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star_align:
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- software/star/align/**
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- tests/software/star/align/**
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star_genomegenerate:
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- software/star/genomegenerate/**
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- tests/software/star/genomegenerate/**
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strelka_germline:
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- software/strelka/germline/**
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- tests/software/strelka/germline/**
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stringtie:
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- software/stringtie/**
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- tests/software/stringtie/**
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tabix_bgzip:
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- software/tabix/bgzip/**
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- tests/software/tabix/bgzip/**
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tabix_tabix:
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- software/tabix/tabix/**
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- tests/software/tabix/tabix/**
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tiddit_sv:
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- software/tiddit/sv/**
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- tests/software/tiddit/sv/**
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trimgalore:
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- software/trimgalore/**
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- tests/software/trimgalore/**
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ucsc_bed12tobigbed:
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- software/ucsc/bed12tobigbed/**
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- tests/software/ucsc/bed12tobigbed/**
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ucsc_bedgraphtobigwig:
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- software/ucsc/bedgraphtobigwig/**
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- tests/software/ucsc/bedgraphtobigwig/**
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unicycler:
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- software/unicycler/**
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- tests/software/unicycler/**
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untar:
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- software/untar/**
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- tests/software/untar/**
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vcftools:
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- software/vcftools/**
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- tests/software/vcftools/**
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yara:
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- software/yara/mapper/**
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- tests/software/yara/mapper/**
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yara_index:
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- software/yara/index/**
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- tests/software/yara/index/**
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