(Modified) Add flag to only compile workflow to cwl without running (#…

…274)

Co-authored-by: JesseMckinzie <jessemckinzie145@gmail.com>

src/sophios/cli.py

@@ -83,6 +83,8 @@
                        help='Just generates run.sh and exits. Does not actually invoke ./run.sh')
 group_run.add_argument('--run_local', default=False, action="store_true",
                        help='After generating the cwl file(s), run it on your local machine.')
+group_run.add_argument('--generate_cwl_workflow', required=False, default=False, action="store_true",
+                       help='Compile the workflow without pulling the docker image')
 
 parser.add_argument('--cwl_inline_subworkflows', default=False, action="store_true",
                     help='Before generating the cwl file, inline all subworkflows.')

src/sophios/main.py

@@ -194,6 +194,9 @@ def main() -> None:
             print("(This may happen if you installed the graphviz python package")
             print("but not the graphviz system package.)")
 
+    if args.generate_cwl_workflow:
+        io.write_to_disk(rose_tree, Path('autogenerated/'), True, args.inputs_file)
+
     if args.run_local or args.generate_run_script:
         # cwl-docker-extract recursively `docker pull`s all images in all subworkflows.
         # This is important because cwltool only uses `docker run` when executing