Merge pull request #84 from wfcommons/nextflow_improvements

Nextflow improvements

Author: rafaelfsilva

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

…lator/templates/cwl_templates/folder.cwl …ench/translator/templates/cwl/folder.cwlwfcommons/wfbench/translator/templates/cwl_templates/folder.cwl renamed to wfcommons/wfbench/translator/templates/cwl/folder.cwl wfcommons/wfbench/translator/templates/cwl_templates/folder.cwl renamed to wfcommons/wfbench/translator/templates/cwl/folder.cwl

@@ -49,6 +49,7 @@
 
 try:
     flowcept_agent.stop()
+    time.sleep(5)
 except Exception:
     import traceback
     traceback.print_exc()