From b98f91239b0e7faef7b58d129c90be853137b9d2 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Sat, 28 Oct 2017 16:27:22 -0500
Subject: [PATCH] trimgalore bug
---
preproc_fastq/trimgalore.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index f53cfeb..2c27f5a 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -27,11 +27,11 @@ if [[ -z $pair_id ]] || [[ -z $fq1 ]]; then
usage
fi
-r1base="${r1%.fastq*}"
-r2base="${r2%.fastq*}"
+r1base="${fq1%.fastq*}"
+r2base="${fq2%.fastq*}"
module load trimgalore/0.4.1 cutadapt/1.9.1
-if [ $R1 == $R2 ]
+if [ $fq1 == $fq2 ]
then
trim_galore -q 25 --illumina --gzip --length 35 ${fq1}
mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
--
GitLab