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38 lines
1 KiB
Text
38 lines
1 KiB
Text
process SEQTK_SUBSEQ {
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tag '$sequences'
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label 'process_low'
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conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
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container "${ 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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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 args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: ''
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def ext = "fa"
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if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
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ext = "fq"
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}
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"""
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seqtk \\
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subseq \\
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$args \\
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$sequences \\
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$filter_list | \\
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gzip --no-name > ${sequences}${prefix}.${ext}.gz
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cat <<-END_VERSIONS > versions.yml
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"${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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