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7bfbce94b0
* Added fq/lint module Additions: - fq/lint module, which checks paired end FASTQ files and confirms they are valid. Relates to #1967 * fq/lint linting * Correct Singularity image Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
33 lines
924 B
Text
33 lines
924 B
Text
process FQ_LINT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::fq=0.9.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fq:0.9.1--h9ee0642_0':
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'quay.io/biocontainers/fq:0.9.1--h9ee0642_0' }"
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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("*.fq_lint.txt"), emit: lint
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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 ?: "${meta.id}"
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"""
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fq lint \\
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$args \\
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$fastq > ${prefix}.fq_lint.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fq: \$(echo \$(fq lint --version | sed 's/fq-lint //g'))
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END_VERSIONS
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"""
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}
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