Don't copy output to outdir if not using cwltool (PolusAI#319)

* fix upload-artifcat to v4

* Don't copy output to outdir if not using cwltool

---------

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

Author: vjaganat90

src/sophios/api/pythonapi.py

@@ -797,7 +797,7 @@ def run(self) -> None:
 
         # Finally, since there is an output file copying bug in cwltool,
         # we need to copy the output files manually. See comment above.
-        if args.copy_output_files:
+        if args.cwl_runner == 'cwltool' and args.copy_output_files:
             run_local_module.copy_output_files(self.process_name)
 
 # Process = Union[Step, Workflow]

src/sophios/main.py

@@ -203,7 +203,7 @@ def main() -> None:
 
         # Finally, since there is an output file copying bug in cwltool,
         # we need to copy the output files manually. See comment above.
-        if args.copy_output_files:
+        if args.cwl_runner == 'cwltool' and args.copy_output_files:
             run_local.copy_output_files(yaml_stem)
 
 

tests/test_examples.py

@@ -230,7 +230,7 @@ def run_workflows(yml_path_str: str, yml_path: Path, cwl_runner: str, args: argp
 
     # Finally, since there is an output file copying bug in cwltool,
     # we need to copy the output files manually. See comment above.
-    if args.copy_output_files:
+    if args.cwl_runner == 'cwltool' and args.copy_output_files:
         sophios.run_local.copy_output_files(yaml_stem)