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fc4f3e8822
* add seqsero2 module * correct lint errors * Update modules/seqsero2/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * set output directory Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
45 lines
1.6 KiB
Text
45 lines
1.6 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 SEQSERO2 {
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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::seqsero2=1.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0"
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} else {
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container "quay.io/biocontainers/seqsero2:1.2.1--py_0"
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}
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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("results/*_log.txt") , emit: log
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tuple val(meta), path("results/*_result.tsv"), emit: tsv
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tuple val(meta), path("results/*_result.txt"), emit: txt
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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}" : "${meta.id}"
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"""
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SeqSero2_package.py \\
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$options.args \\
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-d results/ \\
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-n $prefix \\
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-p $task.cpus \\
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-i $seqs
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
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END_VERSIONS
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"""
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}
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