nf-core_modules/modules/bakta/main.nf
Jasmin F 77a6dd3f61
Fix bakta: variable in main.nf (#2050)
Fix variable prodigal_tf
2022-09-13 13:03:21 +02:00

72 lines
2.3 KiB
Text

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_tf = 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
"""
}