diff --git a/biobakery_workflows/utilities.py b/biobakery_workflows/utilities.py index 11ee53e..008138a 100644 --- a/biobakery_workflows/utilities.py +++ b/biobakery_workflows/utilities.py @@ -496,16 +496,17 @@ def run_halla_on_input_file_set(workflow,feature_tasks_info,metadata,output,hall if "gene" in run_type: continue - current_target=os.path.join(os.path.abspath(output),"halla_"+run_type,"hallagram.png") + optional_target=os.path.join(os.path.abspath(output),"halla_"+run_type,"hallagram.png") + always_target=os.path.join(os.path.abspath(output),"halla_"+run_type,"all_associations.txt") halla_tasks.append( workflow.add_task( "halla -x [depends[0]] -y [depends[1]] -o [args[0]]", depends=[infiles[0], metadata], - targets=current_target, - args=os.path.dirname(current_target), + targets=always_target, + args=os.path.dirname(always_target), name="HAllA_{0}".format(run_type))) - halla_tasks_info[run_type]=current_target + halla_tasks_info[run_type]=optional_target return halla_tasks, halla_tasks_info