process STRELKA_SOMATIC { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/strelka:2.9.10--h9ee0642_1' : 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" input: 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 fasta path fai path target_bed path target_bed_tbi output: tuple val(meta), path("*.somatic_indels.vcf.gz") , emit: vcf_indels tuple val(meta), path("*.somatic_indels.vcf.gz.tbi"), emit: vcf_indels_tbi tuple val(meta), path("*.somatic_snvs.vcf.gz") , emit: vcf_snvs tuple val(meta), path("*.somatic_snvs.vcf.gz.tbi") , emit: vcf_snvs_tbi path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : "" def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : "" """ configureStrelkaSomaticWorkflow.py \\ --tumor $input_tumor \\ --normal $input_normal \\ --referenceFasta $fasta \\ $options_target_bed \\ $options_manta \\ $args \\ --runDir strelka python strelka/runWorkflow.py -m local -j $task.cpus mv strelka/results/variants/somatic.indels.vcf.gz ${prefix}.somatic_indels.vcf.gz mv strelka/results/variants/somatic.indels.vcf.gz.tbi ${prefix}.somatic_indels.vcf.gz.tbi mv strelka/results/variants/somatic.snvs.vcf.gz ${prefix}.somatic_snvs.vcf.gz mv strelka/results/variants/somatic.snvs.vcf.gz.tbi ${prefix}.somatic_snvs.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": strelka: \$( configureStrelkaSomaticWorkflow.py --version ) END_VERSIONS """ }