nextflow support improvments

Author: rafaelfsilva

docs/source/dev_api_wfbench.rst

@@ -15,7 +15,7 @@ wfcommons.wfbench.bench
    :noindex:
 
 wfcommons.wfbench.translator.nextflow
-------------------------------------
+-------------------------------------
 
 .. automodule:: wfcommons.wfbench.translator.nextflow
    :members:

docs/source/generating_workflows.rst

@@ -25,6 +25,7 @@ synthetic workflow instances. The current list of available workflow recipes inc
 - :class:`~wfcommons.wfchef.recipes.epigenomics.recipe.EpigenomicsRecipe`: :code:`from wfcommons.wfchef.recipes import EpigenomicsRecipe`
 - :class:`~wfcommons.wfchef.recipes.genome.recipe.GenomeRecipe`: :code:`from wfcommons.wfchef.recipes import GenomeRecipe`
 - :class:`~wfcommons.wfchef.recipes.montage.recipe.MontageRecipe`: :code:`from wfcommons.wfchef.recipes import MontageRecipe`
+- :class:`~wfcommons.wfchef.recipes.rnaseq.recipe.RnaseqRecipe`: :code:`from wfcommons.wfchef.recipes import RnaseqRecipe`
 - :class:`~wfcommons.wfchef.recipes.seismology.recipe.SeismologyRecipe`: :code:`from wfcommons.wfchef.recipes import SeismologyRecipe`
 - :class:`~wfcommons.wfchef.recipes.soykb.recipe.SoykbRecipe`: :code:`from wfcommons.wfchef.recipes import SoykbRecipe`
 - :class:`~wfcommons.wfchef.recipes.srasearch.recipe.SrasearchRecipe`: :code:`from wfcommons.wfchef.recipes import SrasearchRecipe`

docs/source/parsing_logs.rst

@@ -54,6 +54,14 @@ wfcommons.wfchef.recipes.montage.recipe
    :undoc-members:
    :show-inheritance:
 
+wfcommons.wfchef.recipes.rnaseq.recipe
+--------------------------------------
+
+.. automodule:: wfcommons.wfchef.recipes.rnaseq.recipe
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 wfcommons.wfchef.recipes.seismology.recipe
 ------------------------------------------
 

docs/source/user_api_wfchef.rst

@@ -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
@@ -41,7 +41,7 @@ def task(self) -> Task:
             energy=100,
             avg_power=1.0,
             priority=100,
-            executedAt="2024-09-15T08:59:33.699321-04:00",
+            executed_at="2024-09-15T08:59:33.699321-04:00",
             task_type=TaskType.COMPUTE,
             launch_dir="/tmp",
         )

tests/unit/common/test_task.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
@@ -11,6 +11,7 @@
 import pathlib
 import pytest
 
+from datetime import datetime
 from wfcommons.common import Task, Workflow
 from wfcommons.version import __version__, __schema_version__
 
@@ -28,7 +29,8 @@ class TestWorkflow:
     def workflow(self) -> Workflow:
         return Workflow(
             name="Workflow Test",
-            makespan=100.0
+            makespan=100.0,
+            executed_at=str(datetime.now().astimezone().isoformat())
         )
 
     @pytest.mark.unit

tests/unit/common/test_workflow.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2023 The WfCommons Team.
+# Copyright (c) 2020-2025 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

wfcommons/common/task.py

@@ -84,7 +84,7 @@ def __init__(self,
         self.tasks_children = {}
         self.workflow_id: str = None
         self.workflow_json = {}
-        super().__init__(name=name, makespan=self.makespan, executedat=self.executed_at)
+        super().__init__(name=name, makespan=self.makespan, executed_at=self.executed_at)
 
     def add_task(self, task: Task) -> None:
         """

wfcommons/common/workflow.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021 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
@@ -230,7 +230,7 @@ def create_recipe(path_to_instances: Union[str, pathlib.Path],
     :param verbose: when set, prints status messages.
     :type cutoff: bool
     :param verbose: number of times to repeat the err calculation process (due to randomization).
-    :type runs:bool
+    :type runs: bool
     """
     camelname = capitalcase(wf_name)
     savedir.mkdir(exist_ok=True, parents=True)

wfcommons/wfchef/chef.py

@@ -1,21 +1,20 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021 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 .blast import BlastRecipe
+from .bwa import BwaRecipe
+from .cycles import CyclesRecipe
 from .epigenomics import EpigenomicsRecipe
+from .genome import GenomeRecipe
 from .montage import MontageRecipe
-from .cycles import CyclesRecipe
+from .rnaseq import RnaseqRecipe
 from .seismology import SeismologyRecipe
 from .soykb import SoykbRecipe
 from .srasearch import SrasearchRecipe
-
-from .genome import GenomeRecipe
-from .blast import BlastRecipe
-from .bwa import BwaRecipe
-from .rnaseq import RnaseqRecipe