process GFFREAD { tag "$gff" label 'process_low' conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : 'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }" input: path gff output: path "*.gtf" , emit: gtf path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${gff.baseName}" """ gffread \\ $gff \\ $args \\ -o ${prefix}.gtf cat <<-END_VERSIONS > versions.yml "${task.process}": gffread: \$(gffread --version 2>&1) END_VERSIONS """ }