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61 lines
2.4 KiB
Text
61 lines
2.4 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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def options = initOptions(params.options)
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process RSEM_CALCULATEEXPRESSION {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-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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output:
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tuple val(meta), path("*.genes.results") , emit: counts_gene
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tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
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tuple val(meta), path("*.stat") , emit: stat
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tuple val(meta), path("*.log") , emit: logs
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path "*.version.txt" , emit: version
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tuple val(meta), path("*.STAR.genome.bam") , optional:true, emit: bam_star
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tuple val(meta), path("${prefix}.genome.bam") , optional:true, emit: bam_genome
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tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
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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 strandedness = ''
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if (meta.strandedness == 'forward') {
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strandedness = '--strandedness forward'
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} else if (meta.strandedness == 'reverse') {
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strandedness = '--strandedness reverse'
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}
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def paired_end = meta.single_end ? "" : "--paired-end"
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"""
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INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
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rsem-calculate-expression \\
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--num-threads $task.cpus \\
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--temporary-folder ./tmp/ \\
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$strandedness \\
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$paired_end \\
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$options.args \\
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$reads \\
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\$INDEX \\
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$prefix
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rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
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"""
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}
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