millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

Merge pull request #87 from drpatelh/rsem_index

Browse source 
Use STAR to build initial index for RSEM
This commit is contained in:
Harshil Patel 2020-11-30 14:45:32 +00:00 committed by GitHub
commit e02f0de514
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 36 additions and 10 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

46
software/rsem/preparereference/main.nf
View file

@ -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-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
"""
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 {
"""
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
"""
}
}