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90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
42 lines
1.6 KiB
Text
42 lines
1.6 KiB
Text
process PRODIGAL {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
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'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
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input:
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tuple val(meta), path(genome)
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val(output_format)
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output:
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tuple val(meta), path("${prefix}.${output_format}"), emit: gene_annotations
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tuple val(meta), path("${prefix}.fna"), emit: nucleotide_fasta
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tuple val(meta), path("${prefix}.faa"), emit: amino_acid_fasta
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tuple val(meta), path("${prefix}_all.txt"), emit: all_gene_annotations
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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pigz -cdf ${genome} | prodigal \\
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$args \\
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-f $output_format \\
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-d "${prefix}.fna" \\
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-o "${prefix}.${output_format}" \\
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-a "${prefix}.faa" \\
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-s "${prefix}_all.txt"
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
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pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
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END_VERSIONS
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"""
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}
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