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
    """
}