process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) path fasta path fai path dict path germline_resource path germline_resource_tbi path panel_of_normals path panel_of_normals_tbi output: tuple val(meta), path("*.vcf.gz") , emit: vcf tuple val(meta), path("*.tbi") , emit: tbi tuple val(meta), path("*.stats") , emit: stats tuple val(meta), path("*.f1r2.tar.gz"), optional:true, emit: f1r2 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 inputs = input.collect{ "--input $it"}.join(" ") def interval_command = intervals ? "--intervals $intervals" : "" def pon_command = panel_of_normals ? "--panel-of-normals $panel_of_normals" : "" def gr_command = germline_resource ? "--germline-resource $germline_resource" : "" def avail_mem = 3 if (!task.memory) { log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" Mutect2 \\ $inputs \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ $pon_command \\ $gr_command \\ $interval_command \\ --tmp-dir . \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.vcf.gz touch ${prefix}.tbi touch ${prefix}.stats touch ${prefix}.f1r2.tar.gz cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }