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e621f78757
* Update salmon/quant to provide '--libType A' option * Modify lib_type description to be a string * Update tests * lyb_type can be explicitly overwrite * Update main.nf * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
77 lines
2.5 KiB
Text
77 lines
2.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process SALMON_QUANT {
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tag "$meta.id"
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label "process_medium"
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publishDir "${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::salmon=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/salmon:1.4.0--hf69c8f4_0"
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} else {
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container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
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}
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input:
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tuple val(meta), path(reads)
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path index
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path gtf
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path transcript_fasta
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val alignment_mode
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val lib_type
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def reference = "--index $index"
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def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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if (alignment_mode) {
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reference = "-t $transcript_fasta"
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input_reads = "-a $reads"
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}
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def strandedness_opts = [
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'A', 'U', 'SF', 'SR',
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'IS', 'IU' , 'ISF', 'ISR',
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'OS', 'OU' , 'OSF', 'OSR',
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'MS', 'MU' , 'MSF', 'MSR'
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]
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def strandedness = 'A'
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if (lib_type) {
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if (strandedness_opts.contains(lib_type)) {
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strandedness = lib_type
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} else {
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log.info "[Salmon Quant] Invalid library type specified '--libType=${lib_type}', defaulting to auto-detection with '--libType=A'."
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}
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} else {
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strandedness = meta.single_end ? 'U' : 'IU'
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if (meta.strandedness == 'forward') {
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strandedness = meta.single_end ? 'SF' : 'ISF'
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} else if (meta.strandedness == 'reverse') {
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strandedness = meta.single_end ? 'SR' : 'ISR'
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}
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}
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"""
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salmon quant \\
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--geneMap $gtf \\
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--threads $task.cpus \\
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--libType=$strandedness \\
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$reference \\
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$input_reads \\
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$options.args \\
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-o $prefix
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salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
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"""
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}
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