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Nextflow improvements #84

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Merged
rafaelfsilva merged 3 commits into from
Jul 4, 2025
Merged

Nextflow improvements #84

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9ea67a2
Nextflow with Flowcept
rafaelfsilva Jul 4, 2025
9b287d6
Nextflow with Flowcept
rafaelfsilva Jul 4, 2025
e8fcd4c
Nextflow with Flowcept
rafaelfsilva Jul 4, 2025
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2 changes: 1 addition & 1 deletion wfcommons/wfbench/translator/nextflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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0 ...slator/templates/cwl_templates/folder.cwl → ...bench/translator/templates/cwl/folder.cwl
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0 ...nslator/templates/cwl_templates/shell.cwl → ...fbench/translator/templates/cwl/shell.cwl
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0 ...lator/templates/cwl_templates/wfbench.cwl → ...ench/translator/templates/cwl/wfbench.cwl
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1 change: 1 addition & 0 deletions wfcommons/wfbench/translator/templates/flowcept_agent.py
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Expand Up @@ -49,6 +49,7 @@

try:
flowcept_agent.stop()
time.sleep(5)
except Exception:
import traceback
traceback.print_exc()
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