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77a2895785
* initial commit [ci skip] * remove todo from the module files [ci skip] * add a sample test case [ci skip] * push the latest work [ci skip] * bump kleborate build * test passing with the new build for kleborate [ci skip] * ready for review * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process KLEBORATE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1"
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} else {
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container "quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1"
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}
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input:
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tuple val(meta), path(fastas)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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kleborate \\
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$options.args \\
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--outfile ${prefix}.results.txt \\
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--assemblies *.fasta
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echo \$(kleborate -v 2>&1) | sed 's/kleborate //;' > ${software}.version.txt
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"""
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}
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