process STRINGTIE_MERGE {
    label 'process_medium'

    // Note: 2.7X indices incompatible with AWS iGenomes.
    conda     (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"

    input:
    path stringtie_gtf
    path annotation_gtf

    output:
    path "stringtie.merged.gtf", emit: gtf
    path  "versions.yml"       , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def args = task.ext.args ?: ''
    """
    stringtie \\
        --merge $stringtie_gtf \\
        -G $annotation_gtf \\
        -o stringtie.merged.gtf

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        stringtie: \$(stringtie --version 2>&1)
    END_VERSIONS
    """
}