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https://github.com/MillironX/nf-core_modules.git
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f20c427339
* added classic mlst module * removed nf-core TODO comments * included drpatelh suggestions * adjust version capture identation * update main to pass lint * follow output expected by test.yml * suggested prefix change from rpetit3 * Apply suggestions from code review Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.3 KiB
Text
42 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process MLST {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::mlst=2.19.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1"
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} else {
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container "quay.io/biocontainers/mlst:2.19.0--hdfd78af_1"
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}
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path("*.tsv"), emit: tsv
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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mlst \\
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--threads $task.cpus \\
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$fasta \\
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> ${prefix}.tsv
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
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END_VERSIONS
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"""
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}
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