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46 lines
1.4 KiB
Text
46 lines
1.4 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 STAR_GENOMEGENERATE {
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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:getSoftwareName(task.process), publish_id:'') }
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// Note: 2.7X indices incompatible with AWS iGenomes.
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conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
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} else {
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container "quay.io/biocontainers/star:2.6.1d--0"
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}
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input:
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path fasta
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path gtf
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output:
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path "star" , emit: index
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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 memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
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"""
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mkdir star
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STAR \\
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--runMode genomeGenerate \\
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--genomeDir star/ \\
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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.args
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STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
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"""
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}
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