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f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
53 lines
2.2 KiB
Text
53 lines
2.2 KiB
Text
process STRELKA_SOMATIC {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' :
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'quay.io/biocontainers/strelka:2.9.10--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), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index)
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path fasta
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path fai
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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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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_target_bed = target_bed ? "--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 $input_tumor \\
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--normal $input_normal \\
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--referenceFasta $fasta \\
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${options_target_bed} \\
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${options_manta} \\
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$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 ${prefix}.somatic_snvs.vcf.gz.tbi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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strelka: \$( configureStrelkaSomaticWorkflow.py --version )
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END_VERSIONS
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"""
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}
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