filter option trimgalore

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