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https://github.com/MillironX/nf-core_modules.git
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ad46010385
* added module csvtk/split * removed todo statement * adjusted meta map names * changed tests to use generic input files * added module in pytest * updated test-data paths * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
1.8 KiB
Text
50 lines
1.8 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 CSVTK_SPLIT {
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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::csvtk=0.23.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0"
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} else {
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container "quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0"
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}
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input:
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tuple val(meta), path(csv)
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val in_format
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val out_format
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output:
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tuple val(meta), path("*.${out_extension}"), emit: split_csv
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def delimiter = in_format == "tsv" ? "--tabs" : (in_format == "csv" ? "--delimiter ',' " : in_format)
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def out_delimiter = out_format == "tsv" ? "--out-tabs" : (out_format == "csv" ? "--out-delimiter ',' " : out_format)
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out_extension = out_format == "tsv" ? 'tsv' : 'csv'
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"""
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sed -i.bak '/^##/d' $csv
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csvtk \\
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split \\
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$options.args \\
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--num-cpus $task.cpus \\
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$delimiter \\
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$out_delimiter \\
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$csv
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$( csvtk version | sed -e 's/csvtk v//g' ))
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END_VERSIONS
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"""
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}
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