From 5332c4bf516e55885e54db31243229e2aa149b80 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 20 Jul 2020 09:03:40 -0500
Subject: [PATCH] update trim for se
---
preproc_fastq/trimgalore.sh | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index 36e64d5..5cf4f83 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -31,7 +31,6 @@ fi
fqs=''
i=0
numfq=$#
-
while [[ $i -le $numfq ]]
do
fqs="$fqs $1"
@@ -51,17 +50,23 @@ then
fi
numfq=${#fqs[@]}
-
+copts='-q 25 --illumina --gzip --length 35'
+if [[ $numfq == 2 ]]
+then
+ copts="$copts --paired"
+fi
+
source /etc/profile.d/modules.sh
module load trimgalore/0.6.4 cutadapt/2.5
-if [ $numfq > 1 ]
+trim_galore $copts ${fqs}
+files=`find ./ -name "*_val_1.fq.gz"`
+
+if [[ -n $files ]]
then
- trim_galore --paired -q 25 --illumina --gzip --length 35 ${fqs}
mv *_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
mv *_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
else
- trim_galore -q 25 --illumina --gzip --length 35 ${fqs}
mv *_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
fi
--
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