Add alternative input file name pattern

Adapting_new_script_for_computing_cluster.sh

@@ -51,6 +51,23 @@ submit() {
 		fi
 		"${MXQSUB[@]}" --stdout "$log_dir/$id.out" "$0" --execute "$id" "$f1" "$f2"
 	done
+
+	# input files "blabla_R1_001.fastq" , ""blabla_R2_001.fastq"
+	#
+	#  --> id "blabla"
+	#  --> f1 "blabla_R1_001.fastq"
+	#  --> f2 "blabla_R2_001.fastq"
+
+	for f1 in $fastq_dir/*_R1_001.fastq; do
+		id=$(basename ${f1%%_R1_001.fastq})
+		f1=${id}_R1_001.fastq
+		f2=${id}_R2_001.fastq
+		if [ ! -e $fastq_dir/$f2 ]; then
+			echo "no _R2_001.fastq file for $f1"
+			continue
+		fi
+		"${MXQSUB[@]}" --stdout "$log_dir/$id.out" "$0" --execute "$id" "$f1" "$f2"
+	done
 }
 
 execute() {