process PROKKA { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::prokka=1.14.6" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl526_0' : 'quay.io/biocontainers/prokka:1.14.6--pl526_0' }" input: tuple val(meta), path(fasta) path proteins path prodigal_tf output: tuple val(meta), path("${prefix}/*.gff"), emit: gff tuple val(meta), path("${prefix}/*.gbk"), emit: gbk tuple val(meta), path("${prefix}/*.fna"), emit: fna tuple val(meta), path("${prefix}/*.faa"), emit: faa tuple val(meta), path("${prefix}/*.ffn"), emit: ffn tuple val(meta), path("${prefix}/*.sqn"), emit: sqn tuple val(meta), path("${prefix}/*.fsa"), emit: fsa tuple val(meta), path("${prefix}/*.tbl"), emit: tbl tuple val(meta), path("${prefix}/*.err"), emit: err tuple val(meta), path("${prefix}/*.log"), emit: log tuple val(meta), path("${prefix}/*.txt"), emit: txt tuple val(meta), path("${prefix}/*.tsv"), emit: tsv path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def proteins_opt = proteins ? "--proteins ${proteins[0]}" : "" def prodigal_tf = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : "" """ prokka \\ $args \\ --cpus $task.cpus \\ --prefix $prefix \\ $proteins_opt \\ $prodigal_tf \\ $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //') END_VERSIONS """ }