options trimgalore

preproc_fastq/trimgalore.sh

 #!/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