process BAKTA { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::bakta=1.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bakta:1.5.0--pyhdfd78af_0' : 'quay.io/biocontainers/bakta:1.5.0--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) path db path proteins path prodigal_tf output: tuple val(meta), path("${prefix}.embl") , emit: embl tuple val(meta), path("${prefix}.faa") , emit: faa tuple val(meta), path("${prefix}.ffn") , emit: ffn tuple val(meta), path("${prefix}.fna") , emit: fna tuple val(meta), path("${prefix}.gbff") , emit: gbff tuple val(meta), path("${prefix}.gff3") , emit: gff tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa tuple val(meta), path("${prefix}.tsv") , emit: tsv tuple val(meta), path("${prefix}.txt") , emit: txt 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_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : "" """ bakta \\ $args \\ --threads $task.cpus \\ --prefix $prefix \\ --db $db \\ $proteins_opt \\ $prodigal_tf \\ $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' ) END_VERSIONS """ stub: prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.embl touch ${prefix}.faa touch ${prefix}.ffn touch ${prefix}.fna touch ${prefix}.gbff touch ${prefix}.gff3 touch ${prefix}.hypotheticals.tsv touch ${prefix}.hypotheticals.faa touch ${prefix}.tsv touch ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": bakta: \$( echo \$(bakta --version 2>&1) | sed 's/^.*bakta //' ) END_VERSIONS """ }