process BIOBAMBAM_BAMMARKDUPLICATES2 { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::biobambam=2.0.182" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.182--h7d875b9_0': 'quay.io/biocontainers/biobambam:2.0.182--h7d875b9_0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam") , emit: bam tuple val(meta), path("*.metrics.txt"), emit: metrics 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}" """ bammarkduplicates2 \\ $args \\ I=$bam \\ O=${prefix}.bam \\ M=${prefix}.metrics.txt \\ tmpfile=$prefix \\ markthreads=$task.cpus cat <<-END_VERSIONS > versions.yml "${task.process}": bammarkduplicates2: \$(echo \$(bammarkduplicates2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) END_VERSIONS """ }