process MANTA_GERMLINE { tag "$meta.id" label 'process_high' conda (params.enable_conda ? "bioconda::manta=1.6.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/manta:1.6.0--h9ee0642_1' : 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" input: //Matching the target bed with the input sample allows to parallelize the same sample run across different intervals or a single bed file tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi) path fasta path fasta_fai output: tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf tuple val(meta), path("*candidate_small_indels.vcf.gz.tbi"), emit: candidate_small_indels_vcf_tbi tuple val(meta), path("*candidate_sv.vcf.gz") , emit: candidate_sv_vcf tuple val(meta), path("*candidate_sv.vcf.gz.tbi") , emit: candidate_sv_vcf_tbi tuple val(meta), path("*diploid_sv.vcf.gz") , emit: diploid_sv_vcf tuple val(meta), path("*diploid_sv.vcf.gz.tbi") , emit: diploid_sv_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 input_files = input.collect{"--bam ${it}"}.join(' ') def options_manta = target_bed ? "--callRegions $target_bed" : "" """ configManta.py \ ${input_files} \ --reference $fasta \ --runDir manta \ $options_manta \ $args python manta/runWorkflow.py -m local -j $task.cpus mv manta/results/variants/candidateSmallIndels.vcf.gz \ ${prefix}.candidate_small_indels.vcf.gz mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \ ${prefix}.candidate_small_indels.vcf.gz.tbi mv manta/results/variants/candidateSV.vcf.gz \ ${prefix}.candidate_sv.vcf.gz mv manta/results/variants/candidateSV.vcf.gz.tbi \ ${prefix}.candidate_sv.vcf.gz.tbi mv manta/results/variants/diploidSV.vcf.gz \ ${prefix}.diploid_sv.vcf.gz mv manta/results/variants/diploidSV.vcf.gz.tbi \ ${prefix}.diploid_sv.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": manta: \$( configManta.py --version ) END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.candidate_small_indels.vcf.gz touch ${prefix}.candidate_small_indels.vcf.gz.tbi touch ${prefix}.candidate_sv.vcf.gz touch ${prefix}.candidate_sv.vcf.gz.tbi touch ${prefix}.diploid_sv.vcf.gz touch ${prefix}.diploid_sv.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml "${task.process}": manta: \$( configManta.py --version ) END_VERSIONS """ }