From 3090fd6ac9d54dcf227aa362fea8400858d23b42 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 27 Oct 2017 13:09:13 -0500
Subject: [PATCH] options trimgalore
---
preproc_fastq/trimgalore.sh | 33 ++++++++++++++++++++++++++++-----
1 file changed, 28 insertions(+), 5 deletions(-)
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index 0bd2f54..f53cfeb 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -1,20 +1,43 @@
#!/bin/bash
#trimgalore.sh
-pair_id=$1
-read1=$2
-read2=$3
+usage() {
+ echo "-h Help documentation for hisat.sh"
+ echo "-a --FastQ R1"
+ echo "-b --FastQ R2"
+ echo "-p --Prefix for output file name"
+ echo "Example: bash trimgalore.sh -p prefix -a SRR1551047_1.fastq.gz -b SRR1551047_2.fastq.gz"
+ exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :a:b:p:h opt
+do
+ case $opt in
+ a) fq1=$OPTARG;;
+ b) fq2=$OPTARG;;
+ p) pair_id=$OPTARG;;
+ h) usage;;
+ esac
+done
+
+shift $(($OPTIND -1))
+
+# Check for mandatory options
+if [[ -z $pair_id ]] || [[ -z $fq1 ]]; then
+ usage
+fi
+
r1base="${r1%.fastq*}"
r2base="${r2%.fastq*}"
module load trimgalore/0.4.1 cutadapt/1.9.1
if [ $R1 == $R2 ]
then
- trim_galore -q 25 --illumina --gzip --length 35 ${read1}
+ trim_galore -q 25 --illumina --gzip --length 35 ${fq1}
mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
else
- trim_galore --paired -q 25 --illumina --gzip --length 35 ${read1} ${read2}
+ trim_galore --paired -q 25 --illumina --gzip --length 35 ${fq1} ${fq2}
mv ${r1base}_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
mv ${r2base}_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
fi
--
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