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e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
67 lines
2.3 KiB
Text
67 lines
2.3 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 RSEM_PREPAREREFERENCE {
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tag "$fasta"
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label 'process_high'
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publishDir "${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:'index', meta:[:], publish_by_meta:[]) }
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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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path fasta, stageAs: "rsem/*"
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path gtf
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output:
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path "rsem" , emit: index
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path "rsem/*transcripts.fa", emit: transcript_fasta
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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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def args = options.args.tokenize()
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if (args.contains('--star')) {
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args.removeIf { it.contains('--star') }
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def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
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"""
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STAR \\
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--runMode genomeGenerate \\
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--genomeDir rsem/ \\
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--genomeFastaFiles $fasta \\
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--sjdbGTFfile $gtf \\
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--runThreadN $task.cpus \\
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$memory \\
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$options.args2
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rsem-prepare-reference \\
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--gtf $gtf \\
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--num-threads $task.cpus \\
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${args.join(' ')} \\
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$fasta \\
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rsem/genome
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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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} else {
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"""
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rsem-prepare-reference \\
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--gtf $gtf \\
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--num-threads $task.cpus \\
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$options.args \\
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$fasta \\
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rsem/genome
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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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}
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