Created example for importing CWL as an object into python using the parsers in cwl-utils.

Author: alexiswl

README.md

@@ -48,6 +48,44 @@ time.
 python docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl
 ```
 
+### Using the CWL Parsers
+
+```python
+# Imports
+from pathlib import Path
+from ruamel import yaml
+import sys
+
+# File Input - This is the only thing you will need to adjust or take in as an input to your function:
+cwl_file = Path("/path/to/wf.cwl")
+
+# Read in the cwl file from a yaml
+with open(cwl_file, "r") as cwl_h:
+ yaml_obj = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
+    
+# Check CWLVersion
+if 'cwlVersion' not in list(yaml_obj.keys()):
+    print("Error - could not get the cwlVersion")
+    sys.exit(1)
+
+# Import parser based on CWL Version    
+if yaml_obj['cwlVersion'] == 'v1.0':
+    from cwl_utils import parser_v1_0 as parser
+elif yaml_obj['cwlVersion'] == 'v1.1':
+    from cwl_utils import parser_v1_1 as parser
+elif yaml_obj['cwlVersion'] == 'v1.2':
+    from cwl_utils import parser_v1_2 as parser
+else:
+    print("Version error. Did not recognise {} as a CWL version".format(yaml_obj["CWLVersion"]))
+    sys.exit(1)
+
+# Import CWL Object
+cwl_obj = parser.load_document_by_yaml(yaml_obj, cwl_file.as_uri())
+
+# View CWL Object
+print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))
+```
+
 ## Development
 
 ### Regenerate parsers