process GATK4_CALCULATECONTAMINATION { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ 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(pileup), path(matched) val segmentout output: tuple val(meta), path('*.contamination.table'), emit: contamination tuple val(meta), path('*.segmentation.table') , emit: segmentation, optional:true 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 matched_command = matched ? " -matched ${matched} " : '' def segment_command = segmentout ? " -segments ${prefix}.segmentation.table" : '' def avail_mem = 3 if (!task.memory) { log.info '[GATK CalculateContamination] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" CalculateContamination \\ -I $pileup \\ $matched_command \\ -O ${prefix}.contamination.table \\ $segment_command \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }