--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FLASH.sh	Sat Jul 04 08:58:21 2015 -0400
@@ -0,0 +1,41 @@
+#/bin/bash
+
+#grab output files
+merged_reads=$1
+shift
+not_combined_1=$1
+shift
+not_combined_2=$1
+shift
+inter_not_combined=$1
+shift
+reads_and_pairs=$1
+shift
+log_file=$1
+shift
+
+flash $@ > $log_file
+sleep 5 #sleep because phil says so
+
+if [ -f out.notCombined_2.fastq ];
+then
+    mv out.notCombined_2.fastq $not_combined_2
+fi
+if [ -f out.notCombined_1.fastq ];
+then
+    mv out.notCombined_1.fastq $not_combined_1
+fi
+if [ -f out.notCombined.fastq ];
+then
+    mv out.notCombined.fastq $inter_not_combined
+fi
+if [ -f out.readsAndPairs.tab ];
+then
+    mv out.readsAndPairs.tab $reads_and_pairs
+fi
+if [ -f out.extendedFrags.fastq ];
+then
+    mv out.extendedFrags.fastq $merged_reads
+fi
+
+exit 0