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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
54 lines
2.1 KiB
Text
54 lines
2.1 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process STRELKA_GERMLINE {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/strelka:2.9.10--0"
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} else {
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container "quay.io/biocontainers/strelka:2.9.10--0"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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path fasta
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path fai
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path target_bed
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output:
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tuple val(meta), path("*variants.vcf.gz") , emit: vcf
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tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi
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tuple val(meta), path("*genome.vcf.gz") , emit: genome_vcf
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tuple val(meta), path("*genome.vcf.gz.tbi") , emit: genome_vcf_tbi
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def regions = params.target_bed ? "--exome --callRegions ${target_bed}" : ""
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"""
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configureStrelkaGermlineWorkflow.py \\
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--bam $bam \\
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--referenceFasta $fasta \\
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$regions \\
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$options.args \\
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--runDir strelka
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python strelka/runWorkflow.py -m local -j $task.cpus
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mv strelka/results/variants/genome.*.vcf.gz ${prefix}.genome.vcf.gz
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mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi
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mv strelka/results/variants/variants.vcf.gz ${prefix}.variants.vcf.gz
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mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi
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echo configureStrelkaGermlineWorkflow.py --version &> ${software}.version.txt #2>&1
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"""
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}
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