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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
55 lines
2 KiB
Text
Executable file
55 lines
2 KiB
Text
Executable file
// 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 NEXTCLADE {
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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::nextclade_js=0.14.4" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0"
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} else {
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container "quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0"
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}
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input:
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tuple val(meta), path(fasta)
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val output_format
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output:
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tuple val(meta), path("${prefix}.csv") , optional:true, emit: csv
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tuple val(meta), path("${prefix}.json") , optional:true, emit: json
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tuple val(meta), path("${prefix}.tree.json") , optional:true, emit: json_tree
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tuple val(meta), path("${prefix}.tsv") , optional:true, emit: tsv
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tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def format = output_format
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if (!(format in ['json', 'csv', 'tsv', 'tree', 'tsv-clades-only'])) {
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format = 'json'
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}
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def extension = format
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if (format in ['tsv-clades-only']) {
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extension = '.clades.tsv'
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} else if (format in ['tree']) {
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extension = 'tree.json'
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}
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"""
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nextclade \\
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$options.args \\
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--jobs $task.cpus \\
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--input-fasta $fasta \\
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--output-${format} ${prefix}.${extension}
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echo \$(nextclade --version 2>&1) > ${software}.version.txt
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"""
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}
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