Nextflow with Flowcept

Author: rafaelfsilva

wfcommons/wfbench/translator/__init__.py

@@ -1,20 +1,20 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021-2024 The WfCommons Team.
+# Copyright (c) 2021-2025 The WfCommons Team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 
 from .airflow import AirflowTranslator
+from .bash import BashTranslator
+from .cwl import CWLTranslator
 from .dask import DaskTranslator
 from .nextflow import NextflowTranslator
 from .parsl import ParslTranslator
 from .pegasus import PegasusTranslator
+from .pycompss import PyCompssTranslator
 from .swift_t import SwiftTTranslator
 from .taskvine import TaskVineTranslator
-from .cwl import CWLTranslator
-from .bash import BashTranslator
-from .pycompss import PyCompssTranslator

wfcommons/wfbench/translator/cwl.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2024 The WfCommons Team.
+# Copyright (c) 2024-2025 The WfCommons Team.
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -21,6 +21,7 @@
 
 this_dir = pathlib.Path(__file__).resolve().parent
 
+
 class CWLTranslator(Translator):
     """
     A WfFormat parser for creating CWL workflow benchmarks.
@@ -222,9 +223,9 @@ def _write_cwl_files(self, output_folder: pathlib.Path) -> None:
 
         clt_folder = cwl_folder.joinpath("clt")
         clt_folder.mkdir(exist_ok=True)
-        shutil.copy(this_dir.joinpath("templates/cwl_templates/wfbench.cwl"), clt_folder)
-        shutil.copy(this_dir.joinpath("templates/cwl_templates/folder.cwl"), clt_folder)
-        shutil.copy(this_dir.joinpath("templates/cwl_templates/shell.cwl"), clt_folder)
+        shutil.copy(this_dir.joinpath("templates/cwl/wfbench.cwl"), clt_folder)
+        shutil.copy(this_dir.joinpath("templates/cwl/folder.cwl"), clt_folder)
+        shutil.copy(this_dir.joinpath("templates/cwl/shell.cwl"), clt_folder)
 
         with open(cwl_folder.joinpath("main.cwl"), "w", encoding="utf-8") as f:
             f.write("\n".join(self.cwl_script))

wfcommons/wfbench/translator/nextflow.py

@@ -53,8 +53,9 @@ def translate(self, output_folder: pathlib.Path) -> None:
         # Create benchmark files
         self._copy_binary_files(output_folder)
         self._generate_input_files(output_folder)
+        
         if self.workflow.workflow_id:
-            shutil.copy(this_dir.joinpath("templates/nextflow/flowcept_agent.py"), output_folder.joinpath("bin"))
+            shutil.copy(this_dir.joinpath("templates/flowcept_agent.py"), output_folder.joinpath("bin"))
 
         # Create a topological order of the tasks
         sorted_tasks = self._get_tasks_in_topological_order()

wfcommons/wfbench/translator/swift_t.py

@@ -105,7 +105,7 @@ def translate(self, output_folder: pathlib.Path) -> None:
             self.script += f"string fc = sprintf(flowcept, \"{self.workflow.workflow_id}\", \"{self.workflow.name}\", \"{out_files}\");\n" \
                             "python_persist(fc);\n"
 
-        run_workflow_code = self._merge_codelines("templates/swift_t_templates/workflow.swift", self.script)
+        run_workflow_code = self._merge_codelines("templates/swift_t/workflow.swift", self.script)
 
         # write benchmark files
         output_folder.mkdir(parents=True)