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42 lines
1.4 KiB
Text
42 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 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:getSoftwareName(task.process), publish_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.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
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path gtf
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output:
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path "rsem" , 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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"""
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mkdir rsem
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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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