process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" input: tuple val(meta) , path(input) , path(input_index) , val(which_norm) val run_single val run_pon val run_mito val interval_label 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 script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def panels_command = '' def normals_command = '' def inputs_command = '-I ' + input.join( ' -I ') if(run_pon) { panels_command = '' normals_command = '' } else if(run_single) { panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals" normals_command = '' } else if(run_mito){ panels_command = "-L ${interval_label} --mitochondria-mode" normals_command = '' } else { panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz" normals_command = '-normal ' + which_norm.join( ' -normal ') } def avail_mem = 3 if (!task.memory) { log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" Mutect2 \\ -R ${fasta} \\ ${inputs_command} \\ ${normals_command} \\ ${panels_command} \\ -O ${prefix}.vcf.gz \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }