From 7200d63ad80a8918cc9d583c262821bbe9f5ba74 Mon Sep 17 00:00:00 2001 From: Vasu Jaganath Date: Fri, 17 Jan 2025 14:17:26 -0500 Subject: [PATCH] Don't copy output to outdir if not using cwltool --- src/sophios/api/pythonapi.py | 2 +- src/sophios/main.py | 2 +- tests/test_examples.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/sophios/api/pythonapi.py b/src/sophios/api/pythonapi.py index 20f280c4..04d56981 100644 --- 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 index b4332e92..76c8947b 100644 --- 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 index 0318b8a3..65724fc9 100644 --- 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)