version = "0.12.2" container_url = "lbmc/gffread:${version}" params.gffread = "" params.gffread_out = "" process gffread { container = "${container_url}" label "big_mem_mono_cpus" tag "$file_prefix" if (params.gffread_out != "") { publishDir "results/${params.gffread_out}", mode: 'copy' } input: tuple val(file_id), path(gtf) tuple val(fasta_id), path(fasta) output: tuple val(fasta_id), path("${file_prefix}.fasta"), emit: fasta script: if (file_id instanceof List){ file_prefix = file_id[0] } else { file_prefix = file_id } """ gffread ${gtf} -g ${fasta} -x -o ${file_prefix}.fasta """ }