From 8c413eab4c1873a392e127f50ca039a83f50d104 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 7 Feb 2020 13:04:05 -0600
Subject: [PATCH] filter option trimgalore
---
preproc_fastq/trimgalore.sh | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index 1ae8ba1..e1e2966 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -10,12 +10,13 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :a:b:p:h opt
+while getopts :a:b:p:fh opt
do
case $opt in
a) fq1=$OPTARG;;
b) fq2=$OPTARG;;
p) pair_id=$OPTARG;;
+ f) filter=1;;
h) usage;;
esac
done
@@ -42,3 +43,8 @@ else
mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
fi
+
+if [[ $filter == 1 ]]
+then
+ perl $baseDir/parse_trimreport.pl ${pair_id}.trimreport.txt *trimming_report.txt
+fi
--
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