process ELPREP_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': 'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }" input: tuple val(meta), path(bam) output: tuple val(meta), path("**.{bam,sam}"), 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}" if (meta.single_end) { args += " --single-end" } def suffix = args.contains("--output-type sam") ? "sam" : "bam" """ # create directory and move all input so elprep can find and merge them before splitting mkdir input mv ${bam} input/ elprep merge \\ input \\ ${prefix}.${suffix} \\ $args \\ --nr-of-threads $task.cpus cat <<-END_VERSIONS > versions.yml "${task.process}": elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//') END_VERSIONS """ }