process GSTAMA_MERGE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0' : 'quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0' }" input: tuple val(meta), path(bed) path filelist output: tuple val(meta), path("*.bed") , emit: bed tuple val(meta), path("*_gene_report.txt") , emit: gene_report tuple val(meta), path("*_merge.txt") , emit: merge tuple val(meta), path("*_trans_report.txt"), emit: trans_report path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ tama_merge.py \\ -f $filelist \\ -d merge_dup \\ -p ${prefix} \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gstama: \$( tama_merge.py -version | head -n1 ) END_VERSIONS """ }