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60 lines
2.7 KiB
Text
60 lines
2.7 KiB
Text
process MANTA_SOMATIC {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' :
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'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
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input:
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tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_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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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${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 $input_tumor \
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--normalBam $input_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 ${prefix}.somatic_sv.vcf.gz.tbi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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manta: \$( configManta.py --version )
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END_VERSIONS
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"""
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}
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