Merge pull request #22 from KatSteinke/21-fix-configfile

Fix handling of several optional arguments in `run_pipeline.py`

run_magician.py

@@ -187,9 +187,11 @@ def get_snake_cmd(input_file, target: str, profile_type: Optional[str] = DEFAULT
     insert_size = args.insert_size
     cluster_cmd = args.cluster
     snake_cores = args.cores
-    snake_flags = args.snake_flags[0].split()
-    if args.workflow_config_file:
-        default_config_file = pathlib.Path(args.workflow_config_file).resolve()
+    snake_flags = []
+    if args.snake_flags:
+        snake_flags = args.snake_flags[0].split()
+    if args.config_file:
+        default_config_file = pathlib.Path(args.config_file).resolve()
 
     snake_command = get_snake_cmd(community_file, target_result, profiletype, profilename,
                                   read_length, insert_size,