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47 lines
1.2 KiB
Text
47 lines
1.2 KiB
Text
process QCAT {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::qcat=1.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/qcat:1.1.0--py_0' :
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'quay.io/biocontainers/qcat:1.1.0--py_0' }"
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input:
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tuple val(meta), path(reads)
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val barcode_kit
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output:
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tuple val(meta), path("fastq/*.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 ?: "${meta.id}"
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"""
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## Unzip fastq file
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## qcat doesn't support zipped files yet
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FILE=$reads
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if [[ \$FILE == *.gz ]]
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then
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zcat $reads > unzipped.fastq
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FILE=unzipped.fastq
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fi
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qcat \\
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-f \$FILE \\
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-b ./fastq \\
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--kit $barcode_kit
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## Zip fastq files
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gzip fastq/*
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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qcat: \$(qcat --version 2>&1 | sed 's/^.*qcat //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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