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