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1016c9bd1a
* Initial commit of seqtk/seq module files * pytest.yml * updated module and tests code, need to finish modules/main.nf * Initial commit of seqtk/seq module files * pytest.yml * updated module and tests code, need to finish modules/main.nf * Adding code and configs for seqtk/seq module * Re-tested module following minor code update * removed trailing whitespace errors * Changed variable name to following reviewer suggestions Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process SEQTK_SEQ {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
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'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
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input:
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tuple val(meta), path(fastx)
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output:
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tuple val(meta), path("*.gz") , emit: fastx
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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 ?: "${meta.id}"
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def extension = "fastq"
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if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) {
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extension = "fasta"
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}
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"""
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seqtk \\
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seq \\
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$args \\
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$fastx | \\
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gzip -c > ${prefix}.seqtk-seq.${extension}.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seqtk: \$(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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