process STRELKA_GERMLINE { 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--0' : 'quay.io/biocontainers/strelka:2.9.10--0' }" input: tuple val(meta), path(input), path(input_index) path fasta path fai path target_bed path target_bed_tbi output: tuple val(meta), path("*variants.vcf.gz") , emit: vcf tuple val(meta), path("*variants.vcf.gz.tbi"), emit: vcf_tbi tuple val(meta), path("*genome.vcf.gz") , emit: genome_vcf tuple val(meta), path("*genome.vcf.gz.tbi") , emit: genome_vcf_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 regions = target_bed ? "--exome --callRegions ${target_bed}" : "" """ configureStrelkaGermlineWorkflow.py \\ --bam $input \\ --referenceFasta $fasta \\ $regions \\ $args \\ --runDir strelka python strelka/runWorkflow.py -m local -j $task.cpus mv strelka/results/variants/genome.*.vcf.gz ${prefix}.genome.vcf.gz mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi mv strelka/results/variants/variants.vcf.gz ${prefix}.variants.vcf.gz mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": strelka: \$( configureStrelkaGermlineWorkflow.py --version ) END_VERSIONS """ }