kkonganti@0: process PROKKA { kkonganti@0: tag "$meta.id" kkonganti@0: label 'process_low' kkonganti@0: kkonganti@0: module (params.enable_module ? "${params.swmodulepath}${params.fs}prokka${params.fs}1.14.6" : null) kkonganti@0: conda (params.enable_conda ? "bioconda::prokka=1.14.6 conda-forge::perl" : null) kkonganti@0: container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? kkonganti@0: 'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' : kkonganti@0: 'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }" kkonganti@0: kkonganti@0: input: kkonganti@0: tuple val(meta), path(fasta), path(proteins), path(prodigal_tf) kkonganti@0: kkonganti@0: output: kkonganti@0: tuple val(meta), path("${prefix}/*.gff"), emit: gff kkonganti@0: tuple val(meta), path("${prefix}/*.gbk"), emit: gbk kkonganti@0: tuple val(meta), path("${prefix}/*.fna"), emit: fna kkonganti@0: tuple val(meta), path("${prefix}/*.faa"), emit: faa kkonganti@0: tuple val(meta), path("${prefix}/*.ffn"), emit: ffn kkonganti@0: tuple val(meta), path("${prefix}/*.sqn"), emit: sqn kkonganti@0: tuple val(meta), path("${prefix}/*.fsa"), emit: fsa kkonganti@0: tuple val(meta), path("${prefix}/*.tbl"), emit: tbl kkonganti@0: tuple val(meta), path("${prefix}/*.err"), emit: err kkonganti@0: tuple val(meta), path("${prefix}/*.log"), emit: log kkonganti@0: tuple val(meta), path("${prefix}/*.txt"), emit: txt kkonganti@0: tuple val(meta), path("${prefix}/*.tsv"), emit: tsv kkonganti@0: path "versions.yml" , emit: versions kkonganti@0: kkonganti@0: when: kkonganti@0: task.ext.when == null || task.ext.when kkonganti@0: kkonganti@0: script: kkonganti@0: def args = task.ext.args ?: '' kkonganti@0: def proteins_opt = proteins ? "--proteins ${proteins[0]}" : "" kkonganti@0: def prodigal_tf = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : "" kkonganti@0: def prefix_l = "${meta.id}" ?: '' kkonganti@0: prefix = task.ext.prefix ?: "${meta.id}" kkonganti@0: def strain = !params.prokka_strain && prefix_l ? "--strain '${prefix_l}'" : '' kkonganti@0: kkonganti@0: """ kkonganti@0: prokka \\ kkonganti@0: $strain \\ kkonganti@0: $args \\ kkonganti@0: --cpus $task.cpus \\ kkonganti@0: --prefix $prefix \\ kkonganti@0: $proteins_opt \\ kkonganti@0: $prodigal_tf \\ kkonganti@0: $fasta kkonganti@0: kkonganti@0: cat <<-END_VERSIONS > versions.yml kkonganti@0: "${task.process}": kkonganti@0: prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //') kkonganti@0: END_VERSIONS kkonganti@0: """ kkonganti@0: }