From 81cb8e68edb992d050eec76a1bc65bfe683a18ef Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 18 Jan 2020 16:32:34 -0600
Subject: [PATCH] Give trim_galore all cpu's available
---
workflow/rna-seq.nf | 11 ++---------
1 file changed, 2 insertions(+), 9 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d4b917f..68a6516 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -121,21 +121,14 @@ process trimData {
hostname >>${repRID}.trimData.err
ulimit -a >>${repRID}.trimData.err
- if [ `nproc` -gt 8 ]
- then
- ncore=8
- else
- ncore=`nproc`
- fi
-
# trim fastqs
if [ '${fastq[1]}' == 'null' ]
then
ends='se'
- trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j \${ncore} ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
+ trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
else
ends='pe'
- trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j \${ncore} ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
+ trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]} 1>>${repRID}.trimData.log 2>>${repRID}.trimData.err;
fi
"""
}
\ No newline at end of file
--
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