mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
process PLASMIDFINDER {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1':
|
|
'quay.io/biocontainers/plasmidfinder:2.1.6--py310hdfd78af_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(seqs)
|
|
|
|
output:
|
|
tuple val(meta), path("*.json") , emit: json
|
|
tuple val(meta), path("*.txt") , emit: txt
|
|
tuple val(meta), path("*.tsv") , emit: tsv
|
|
tuple val(meta), path("*-hit_in_genome_seq.fsa"), emit: genome_seq
|
|
tuple val(meta), path("*-plasmid_seqs.fsa") , emit: plasmid_seq
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def VERSION = '2.1.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
plasmidfinder.py \\
|
|
$args \\
|
|
-i $seqs \\
|
|
-o ./ \\
|
|
-x
|
|
|
|
# Rename hard-coded outputs with prefix to avoid name collisions
|
|
mv data.json ${prefix}.json
|
|
mv results.txt ${prefix}.txt
|
|
mv results_tab.tsv ${prefix}.tsv
|
|
mv Hit_in_genome_seq.fsa ${prefix}-hit_in_genome_seq.fsa
|
|
mv Plasmid_seqs.fsa ${prefix}-plasmid_seqs.fsa
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
plasmidfinder: $VERSION
|
|
END_VERSIONS
|
|
"""
|
|
}
|