From aaab2a65e8c4385ab82eef90bc83f70574d501e1 Mon Sep 17 00:00:00 2001
From: Mike Smith <grimbough@gmail.com>
Date: Wed, 2 May 2018 18:24:34 +0200
Subject: [PATCH] modifed bwa example

---
 exercises/bwa/bwa_batch.sh | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/exercises/bwa/bwa_batch.sh b/exercises/bwa/bwa_batch.sh
index 375cc4b..4f1d052 100644
--- a/exercises/bwa/bwa_batch.sh
+++ b/exercises/bwa/bwa_batch.sh
@@ -1,6 +1,10 @@
 #!/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/
-- 
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