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754db250a0
* remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
67 lines
3.1 KiB
Text
67 lines
3.1 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 MANTA_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::manta=1.6.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1"
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} else {
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container "quay.io/biocontainers/manta:1.6.0--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)
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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("*.candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf
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tuple val(meta), path("*.candidate_small_indels.vcf.gz.tbi") , emit: candidate_small_indels_vcf_tbi
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tuple val(meta), path("*.candidate_sv.vcf.gz") , emit: candidate_sv_vcf
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tuple val(meta), path("*.candidate_sv.vcf.gz.tbi") , emit: candidate_sv_vcf_tbi
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tuple val(meta), path("*.diploid_sv.vcf.gz") , emit: diploid_sv_vcf
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tuple val(meta), path("*.diploid_sv.vcf.gz.tbi") , emit: diploid_sv_vcf_tbi
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tuple val(meta), path("*.somatic_sv.vcf.gz") , emit: somatic_sv_vcf
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tuple val(meta), path("*.somatic_sv.vcf.gz.tbi") , emit: somatic_sv_vcf_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_manta = target_bed ? "--exome --callRegions $target_bed" : ""
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"""
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configManta.py \
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--tumorBam $cram_tumor \
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--normalBam $cram_normal \
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--reference $fasta \
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$options_manta \
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--runDir manta
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python manta/runWorkflow.py -m local -j $task.cpus
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mv manta/results/variants/candidateSmallIndels.vcf.gz ${prefix}.candidate_small_indels.vcf.gz
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mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi ${prefix}.candidate_small_indels.vcf.gz.tbi
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mv manta/results/variants/candidateSV.vcf.gz ${prefix}.candidate_sv.vcf.gz
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mv manta/results/variants/candidateSV.vcf.gz.tbi ${prefix}.candidate_sv.vcf.gz.tbi
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mv manta/results/variants/diploidSV.vcf.gz ${prefix}.diploid_sv.vcf.gz
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mv manta/results/variants/diploidSV.vcf.gz.tbi ${prefix}.diploid_sv.vcf.gz.tbi
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mv manta/results/variants/somaticSV.vcf.gz ${prefix}.somatic_sv.vcf.gz
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mv manta/results/variants/somaticSV.vcf.gz.tbi ${prefix}.somatic_sv.vcf.gz.tbi
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( configManta.py --version )
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END_VERSIONS
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"""
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}
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