nf-core_modules/modules/rsem/preparereference/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process RSEM_PREPAREREFERENCE {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
} else {
container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
}
input:
path fasta, stageAs: "rsem/*"
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path gtf
output:
path "rsem" , emit: index
path "rsem/*transcripts.fa", emit: transcript_fasta
path "*.version.txt" , emit: version
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script:
def software = getSoftwareName(task.process)
def args = options.args.tokenize()
if (args.contains('--star')) {
args.removeIf { it.contains('--star') }
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
"""
STAR \\
--runMode genomeGenerate \\
--genomeDir rsem/ \\
--genomeFastaFiles $fasta \\
--sjdbGTFfile $gtf \\
--runThreadN $task.cpus \\
$memory \\
$options.args2
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\
${args.join(' ')} \\
$fasta \\
rsem/genome
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
"""
} else {
"""
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\
$options.args \\
$fasta \\
rsem/genome
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
"""
}
}