Don't copy output to outdir if not using cwltool

vjaganat90 · Jan 17, 2025 · 7200d63 · 7200d63
1 parent a25a726
commit 7200d63
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/src/sophios/api/pythonapi.py b/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]
diff --git a/src/sophios/main.py b/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)
 
 

diff --git a/tests/test_examples.py b/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)