process FGBIO_FASTQTOBAM { 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(reads) val read_structure output: tuple val(meta), path("*_umi_converted.bam"), emit: umibam 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 \\ FastqToBam \\ -i $reads \\ -o "${prefix}_umi_converted.bam" \\ --read-structures $read_structure \\ --sample $meta.id \\ --library $meta.id \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//') END_VERSIONS """ }