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53 lines
1.6 KiB
Plaintext
53 lines
1.6 KiB
Plaintext
process SLIMFASTQ {
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tag "$meta.id"
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label 'process_low'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2':
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'quay.io/biocontainers/slimfastq:2.04--h87f3376_2' }"
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input:
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tuple val(meta), path(fastq)
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output:
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tuple val(meta), path("*.sfq"), emit: sfq
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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 ?: "${meta.id}"
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def VERSION = '2.04' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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if (meta.single_end) {
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"""
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gzip -d -c '${fastq}' | slimfastq \\
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$args \\
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-f '${prefix}.sfq'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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slimfastq: ${VERSION}
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END_VERSIONS
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"""
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} else {
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"""
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gzip -d -c '${fastq[0]}' | slimfastq \\
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$args \\
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-f '${prefix}_1.sfq'
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gzip -d -c '${fastq[1]}' | slimfastq \\
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$args \\
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-f '${prefix}_2.sfq'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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slimfastq: ${VERSION}
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END_VERSIONS
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"""
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}
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}
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