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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
48 lines
1.5 KiB
Text
48 lines
1.5 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 SEQTK_SUBSEQ {
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tag '$sequences'
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label 'process_low'
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publishDir "${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:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
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} else {
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container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
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}
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input:
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path sequences
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path filter_list
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output:
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path "*.gz" , emit: sequences
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ?: ''
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def ext = "fa"
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if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
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ext = "fq"
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}
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"""
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seqtk \\
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subseq \\
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$options.args \\
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$sequences \\
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$filter_list | \\
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gzip --no-name > ${sequences}${prefix}.${ext}.gz
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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