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64 lines
1.7 KiB
Plaintext
64 lines
1.7 KiB
Plaintext
process SEQTK_SAMPLE {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
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container "${ 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(reads)
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val sample_size
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output:
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tuple val(meta), path("*.fastq.gz"), emit: reads
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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 ?: "${meta.id}"
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if (meta.single_end) {
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"""
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seqtk \\
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sample \\
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$args \\
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$reads \\
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$sample_size \\
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| gzip --no-name > ${prefix}.fastq.gz \\
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cat <<-END_VERSIONS > versions.yml
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"${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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} else {
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if (!(args ==~ /.*-s[0-9]+.*/)) {
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args += " -s100"
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}
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"""
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seqtk \\
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sample \\
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$args \\
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${reads[0]} \\
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$sample_size \\
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| gzip --no-name > ${prefix}_1.fastq.gz \\
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seqtk \\
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sample \\
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$args \\
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${reads[1]} \\
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$sample_size \\
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| gzip --no-name > ${prefix}_2.fastq.gz \\
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cat <<-END_VERSIONS > versions.yml
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"${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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}
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