fixed file name errors

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/