process PICARD_MARKDUPLICATES { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::picard=2.26.7" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' : 'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.metrics.txt"), emit: metrics path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def avail_mem = 3 if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ picard \\ -Xmx${avail_mem}g \\ MarkDuplicates \\ $args \\ I=$bam \\ O=${prefix}.bam \\ M=${prefix}.MarkDuplicates.metrics.txt cat <<-END_VERSIONS > versions.yml "${task.process}": picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) END_VERSIONS """ }