fix basepath issue in run_cwl_serialized_async and fix erroneous _inline extension (PolusAI#331)

* fix unnecessary/obselete suffix to yaml stem when using inlining

* fix the path issue in python api

---------

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

Author: vjaganat90

src/sophios/run_local.py

@@ -150,7 +150,6 @@ def run_local(args: argparse.Namespace, rose_tree: RoseTree, cachedir: Optional[
     # will cause github to terminate the CI Action...
     skip_schemas = ['--skip-schemas'] if not args.no_skip_dollar_schemas else []
 
-    yaml_stem = yaml_stem + '_inline' if args.cwl_inline_subworkflows else yaml_stem
     if cwl_runner == 'cwltool':
         parallel = ['--parallel'] if args.parallel else []
         # NOTE: --parallel is required for real-time analysis / real-time plots,
@@ -474,13 +473,14 @@ async def run_cwl_serialized_async(workflow: Json, basepath: str,
     compiled_cwl = workflow_name + '.cwl'
     inputs_yml = workflow_name + '_inputs.yml'
     # write _input.yml file
-    with open(Path.cwd() / basepath / inputs_yml, 'w', encoding='utf-8') as f:
+    with open(basepath / inputs_yml, 'w', encoding='utf-8') as f:
         yaml.dump(workflow['yaml_inputs'], f)
     workflow.pop('retval', None)
     workflow.pop('yaml_inputs', None)
     workflow.pop('name', None)
+    basepath = basepath.rstrip("/") if basepath != "/" else basepath
     # write compiled .cwl file
-    with open(Path.cwd() / basepath / compiled_cwl, 'w', encoding='utf-8') as f:
+    with open(basepath / compiled_cwl, 'w', encoding='utf-8') as f:
         yaml.dump(workflow, f)
     retval = run_cwl_workflow(workflow_name, basepath,
                               cwl_runner, container_cmd, False, env_commands=env_commands)