modifed bwa example

exercises/bwa/bwa_batch.sh

 #!/bin/bash
-#SBATCH --mem 150
-#SBATCH --nodes 8
+#SBATCH -t 00:15:00
+#SBATCH --mem=150
+#SBATCH --nodes=1
+
+## copy data to /scratch and change directory
+cp reference.fa reads.txt $SCRATCHDIR && cd $SCRATCHDIR
 
 ## create an index
 bwa index reference.fa
@@ -10,3 +14,6 @@ bwa aln -I reference.fa reads.txt > out.sai
 
 ## create SAM file
 bwa samse reference.fa out.sai reads.txt > out.sam
+
+## copy results back
+cp out.sam $HOME/embl_hpc/exercises/bwa/