process GSTAMA_COLLAPSE { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0' : 'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }" input: tuple val(meta), path(bam) path fasta output: tuple val(meta), path("*_collapsed.bed") , emit: bed tuple val(meta), path("*_trans_read.bed") , emit: bed_trans_reads tuple val(meta), path("*_local_density_error.txt"), emit: local_density_error tuple val(meta), path("*_polya.txt") , emit: polya tuple val(meta), path("*_read.txt") , emit: read tuple val(meta), path("*_strand_check.txt") , emit: strand_check tuple val(meta), path("*_trans_report.txt") , emit: trans_report path "versions.yml" , emit: versions tuple val(meta), path("*_varcov.txt") , emit: varcov , optional: true tuple val(meta), path("*_variants.txt") , emit: variants, optional: true script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ tama_collapse.py \\ -s $bam \\ -f $fasta \\ -p ${prefix} \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' ) END_VERSIONS """ }