process FGBIO_GROUPREADSBYUMI { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' : 'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" input: tuple val(meta), path(taggedbam) val(strategy) output: tuple val(meta), path("*_umi-grouped.bam") , emit: bam tuple val(meta), path("*_umi_histogram.txt"), emit: histogram path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ mkdir tmp fgbio \\ --tmp-dir=${PWD}/tmp \\ GroupReadsByUmi \\ -s $strategy \\ $args \\ -i $taggedbam \\ -o ${prefix}_umi-grouped.bam \\ -f ${prefix}_umi_histogram.txt cat <<-END_VERSIONS > versions.yml "${task.process}": fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//') END_VERSIONS """ }