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43 lines
1.3 KiB
Text
43 lines
1.3 KiB
Text
process CSVTK_SPLIT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' :
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'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }"
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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("*.${out_extension}"), emit: split_csv
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${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' $csv
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csvtk \\
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split \\
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$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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"${task.process}":
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csvtk: \$(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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