From e91b3300b271ce35b32482656994c98dd9f26911 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 13 Aug 2020 09:50:18 -0500
Subject: [PATCH] Remove Illumina addapter trim restriction, set to default
(auto) and limit cores to 4
---
workflow/rna-seq.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 7d5e1d3..2c5e6fd 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -304,11 +304,11 @@ process trimData {
echo -e "LOG: trimming ${ends}" >> ${repRID}.trimData.log
if [ "${ends}" == "se" ]
then
- trim_galore --gzip -q 25 --illumina --length 35 --basename ${repRID} -j `nproc` ${fastq[0]}
+ trim_galore --gzip -q 25 --length 35 --basename ${repRID} -j 4 ${fastq[0]}
readLength=\$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length(\$1)}' | sort -n | awk '{a[NR]=\$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
elif [ "${ends}" == "pe" ]
then
- trim_galore --gzip -q 25 --illumina --length 35 --paired --basename ${repRID} -j `nproc` ${fastq[0]} ${fastq[1]}
+ trim_galore --gzip -q 25 --length 35 --paired --basename ${repRID} -j 4 ${fastq[0]} ${fastq[1]}
readLength=\$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length(\$1)}' | sort -n | awk '{a[NR]=\$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
fi
echo -e "LOG: trimmed" >> ${repRID}.trimData.log
--
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