From 9ea67a292410ad48a47a9e60445c307cfad4cb37 Mon Sep 17 00:00:00 2001 From: Rafael Ferreira da Silva Date: Thu, 3 Jul 2025 20:38:05 -0400 Subject: [PATCH 1/3] Nextflow with Flowcept --- .../translator/templates/{cwl_templates => cwl}/folder.cwl | 0 .../wfbench/translator/templates/{cwl_templates => cwl}/shell.cwl | 0 .../translator/templates/{cwl_templates => cwl}/wfbench.cwl | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename wfcommons/wfbench/translator/templates/{cwl_templates => cwl}/folder.cwl (100%) rename wfcommons/wfbench/translator/templates/{cwl_templates => cwl}/shell.cwl (100%) rename wfcommons/wfbench/translator/templates/{cwl_templates => cwl}/wfbench.cwl (100%) diff --git a/wfcommons/wfbench/translator/templates/cwl_templates/folder.cwl b/wfcommons/wfbench/translator/templates/cwl/folder.cwl similarity index 100% rename from wfcommons/wfbench/translator/templates/cwl_templates/folder.cwl rename to wfcommons/wfbench/translator/templates/cwl/folder.cwl diff --git a/wfcommons/wfbench/translator/templates/cwl_templates/shell.cwl b/wfcommons/wfbench/translator/templates/cwl/shell.cwl similarity index 100% rename from wfcommons/wfbench/translator/templates/cwl_templates/shell.cwl rename to wfcommons/wfbench/translator/templates/cwl/shell.cwl diff --git a/wfcommons/wfbench/translator/templates/cwl_templates/wfbench.cwl b/wfcommons/wfbench/translator/templates/cwl/wfbench.cwl similarity index 100% rename from wfcommons/wfbench/translator/templates/cwl_templates/wfbench.cwl rename to wfcommons/wfbench/translator/templates/cwl/wfbench.cwl From 9b287d6ad36f68515c813acf5426ef370aaae11b Mon Sep 17 00:00:00 2001 From: Rafael Ferreira da Silva Date: Thu, 3 Jul 2025 21:23:01 -0400 Subject: [PATCH 2/3] Nextflow with Flowcept --- wfcommons/wfbench/translator/nextflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wfcommons/wfbench/translator/nextflow.py b/wfcommons/wfbench/translator/nextflow.py index 342e4448..aec23518 100644 --- a/wfcommons/wfbench/translator/nextflow.py +++ b/wfcommons/wfbench/translator/nextflow.py @@ -134,7 +134,7 @@ def _get_tasks_in_topological_order(self) -> List[Task]: for potential_task in all_children: num_children = len(self.task_children[potential_task.task_id]) if not num_children: - self.out_files.add(f"{self.output_folder.absolute()}/{potential_task.output_files[0]}") + self.out_files.add(f"{self.output_folder.absolute()}/data/{potential_task.output_files[0]}") if all(parent in sorted_tasks for parent in self._find_parents(potential_task.task_id)): tasks_in_current_level.append(potential_task) levels[current_level] = tasks_in_current_level From e8fcd4c09406cb4e66045959e855f70ec2274926 Mon Sep 17 00:00:00 2001 From: Rafael Ferreira da Silva Date: Thu, 3 Jul 2025 21:43:05 -0400 Subject: [PATCH 3/3] Nextflow with Flowcept --- wfcommons/wfbench/translator/templates/flowcept_agent.py | 1 + 1 file changed, 1 insertion(+) diff --git a/wfcommons/wfbench/translator/templates/flowcept_agent.py b/wfcommons/wfbench/translator/templates/flowcept_agent.py index 51118a72..a8c77f86 100755 --- a/wfcommons/wfbench/translator/templates/flowcept_agent.py +++ b/wfcommons/wfbench/translator/templates/flowcept_agent.py @@ -49,6 +49,7 @@ try: flowcept_agent.stop() + time.sleep(5) except Exception: import traceback traceback.print_exc()