process PBBAM_PBMERGE { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::pbbam=1.7.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pbbam:1.7.0--h058f120_1' : 'quay.io/biocontainers/pbbam:1.7.0--h058f120_1' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.pbi"), emit: pbi path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ pbmerge \\ -o ${prefix}.bam \\ $args \\ *.bam cat <<-END_VERSIONS > versions.yml "${task.process}": pbbam: \$( pbmerge --version|sed 's/pbmerge //' ) END_VERSIONS """ }