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257078bb39
* add BP to strelka/somatic * merge conflicts * update strelka modules for BP * update strelka modules for BP * apply suggestions from code review
61 lines
2.6 KiB
Text
61 lines
2.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process STRELKA_SOMATIC {
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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--h9ee0642_1"
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} else {
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container "quay.io/biocontainers/strelka:2.9.10--h9ee0642_1"
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}
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input:
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tuple val(meta), path(cram_normal), path(crai_normal), path(cram_tumor), path(crai_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi)
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path fasta
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path fai
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path target_bed
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path target_bed_tbi
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output:
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tuple val(meta), path("*.somatic_indels.vcf.gz") , emit: vcf_indels
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tuple val(meta), path("*.somatic_indels.vcf.gz.tbi"), emit: vcf_indels_tbi
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tuple val(meta), path("*.somatic_snvs.vcf.gz") , emit: vcf_snvs
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tuple val(meta), path("*.somatic_snvs.vcf.gz.tbi") , emit: vcf_snvs_tbi
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : ""
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def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : ""
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"""
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configureStrelkaSomaticWorkflow.py \\
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--tumor $cram_tumor \\
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--normal $cram_normal \\
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--referenceFasta $fasta \\
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$options_target_bed \\
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$options_manta \\
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$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/somatic.indels.vcf.gz ${prefix}.somatic_indels.vcf.gz
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mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}.somatic_indels.vcf.gz.tbi
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mv strelka/results/variants/somatic.snvs.vcf.gz ${prefix}.somatic_snvs.vcf.gz
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mv strelka/results/variants/somatic.snvs.vcf.gz.tbi ${prefix}.somatic_snvs.vcf.gz.tbi
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( configureStrelkaSomaticWorkflow.py --version )
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END_VERSIONS
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"""
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}
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