remove redundant io in main & remove irrelevant warning/exit in compiler (PolusAI#284)

* add user args for workflows built with python api

* remove redundant io in main & remove irrelevant warning/exit in compiler

---------

Co-authored-by: Vasu Jaganath <[email protected]>

Author: vjaganat90

src/sophios/compiler.py

@@ -881,10 +881,6 @@ def compile_workflow_once(yaml_tree_ast: YamlTree,
             new_keyval = {key: newval}
         elif 'Directory' == in_dict['type']:
             if not args.ignore_dir_path:
-                if in_dict['value'].startswith('/'):
-                    print("Warning! directory can not start with '/'")
-                    print("It is most likely an incorrect path! Can't create directories!")
-                    sys.exit(1)
                 ldir = Path(in_dict['value'])
                 if not ldir.is_absolute():
                     ldir = Path('autogenerated') / ldir

src/sophios/main.py

@@ -194,9 +194,6 @@ 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