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a0bc08732c
* added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
51 lines
1.7 KiB
Text
51 lines
1.7 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process FGBIO_FASTQTOBAM {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0"
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}
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input:
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tuple val(meta), path(reads)
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val(read_structure)
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output:
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tuple val(meta), path("*_umi_converted.bam"), emit: umibam
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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mkdir tmpFolder
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fgbio \\
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--tmp-dir=${PWD}/tmpFolder \\
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FastqToBam \\
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-i $reads \\
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-o "${prefix}_umi_converted.bam" \\
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--read-structures $read_structure \\
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--sample $meta.id \\
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--library $meta.id \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
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END_VERSIONS
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"""
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}
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