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 """ }