process FGBIO_CALLMOLECULARCONSENSUSREADS { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' : 'quay.io/biocontainers/fgbio:1.3.0--0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("*.bam"), emit: bam 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}" """ fgbio \\ CallMolecularConsensusReads \\ -i $bam \\ $args \\ -o ${prefix}.bam cat <<-END_VERSIONS > versions.yml "${task.process}": fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//') END_VERSIONS """ }