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Use STAR to build initial index for RSEM

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drpatelh 2020-11-30 11:29:24 +00:00
parent 794a5cbd0c
commit e5c7ecc89c
1 changed files with 36 additions and 10 deletions
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46
software/rsem/preparereference/main.nf
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@ -24,15 +24,41 @@ process RSEM_PREPAREREFERENCE {
script:
def software = getSoftwareName(task.process)
"""
mkdir rsem
rsem-prepare-reference \\
--gtf $gtf \\
--num-threads $task.cpus \\
$options.args \\
$fasta \\
rsem/genome
def args = options.args.tokenize()
if (args.contains('--star')) {
args.removeIf { it.contains('--star') }
def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
"""
mkdir rsem
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
"""
rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
"""
} else {
"""
mkdir rsem
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
"""
}
}