From 2e7f9b264569f36707386293f80caa7ce21b3b2d Mon Sep 17 00:00:00 2001
From: Mike Smith <grimbough@gmail.com>
Date: Wed, 2 May 2018 18:32:35 +0200
Subject: [PATCH] fixed file name errors

---
 exercises/bwa/bwa_batch.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/exercises/bwa/bwa_batch.sh b/exercises/bwa/bwa_batch.sh
index 4f1d052..9540f7a 100644
--- a/exercises/bwa/bwa_batch.sh
+++ b/exercises/bwa/bwa_batch.sh
@@ -4,16 +4,16 @@
 #SBATCH --nodes=1
 
 ## copy data to /scratch and change directory
-cp reference.fa reads.txt $SCRATCHDIR && cd $SCRATCHDIR
+cp reference.fa reads.fq $SCRATCHDIR && cd $SCRATCHDIR
 
 ## create an index
 bwa index reference.fa
 
 ## perform alignment
-bwa aln -I reference.fa reads.txt > out.sai
+bwa aln -I reference.fa reads.fq > out.sai
 
 ## create SAM file
-bwa samse reference.fa out.sai reads.txt > out.sam
+bwa samse reference.fa out.sai reads.fq > out.sam
 
 ## copy results back
 cp out.sam $HOME/embl_hpc/exercises/bwa/
-- 
GitLab