--- a/defuse.xml	Fri Jun 07 20:52:19 2013 -0500
+++ b/defuse.xml	Sun Jun 09 20:30:21 2013 -0500
@@ -226,7 +226,9 @@
 #try
 $ref_dict['gmap_index_directory']
 #except
-\$(dataset_directory)/gmap
+#raw
+$(dataset_directory)/gmap
+#end raw
 #end try
 
 #raw
@@ -597,7 +599,7 @@
 mkdir -p output_dir
 #end if
 ## run defuse.pl
-perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -d data_dir -o output_dir  -p 8
+perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
 ## copy primary results to output datasets
 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi