virtool-workflow 5.5.0a2__py3-none-any.whl → 6.0.0a1__py3-none-any.whl

virtool_workflow/analysis/__init__.py

@@ -1,5 +1 @@
 """Tools for workflows relating to sequence analysis."""
-
-__fixtures__ = [
-    "virtool_workflow.analysis.trim_parameters",
-]

virtool_workflow/analysis/fastqc.py

@@ -397,15 +397,12 @@ def _parse_fastqc(fastqc_path: Path, output_path: Path) -> dict:
 class FastQCRunner(Protocol):
     """A protocol describing callables that can be used to run FastQC."""
 
-    async def __call__(self, paths: ReadPaths) -> dict:
+    async def __call__(self, paths: ReadPaths, output_path: Path) -> dict:
         ...
 
 
 @fixture
-async def fastqc(
-    run_subprocess: RunSubprocess,
-    work_path: Path,
-):
+async def fastqc(run_subprocess: RunSubprocess):
     """
     Provides an asynchronous function that can run FastQC as a subprocess.
 
@@ -441,6 +438,4 @@ async def fastqc(
 
         return _parse_fastqc(temp_path, output_path)
 
-    yield func
-
-    await asyncio.to_thread(shutil.rmtree, temp_path)
+    return func

virtool_workflow/runtime/discover.py

@@ -41,6 +41,9 @@ def load_builtin_fixtures():
 
     """
     import_module("virtool_workflow.data")
+    import_module("virtool_workflow.analysis.fastqc")
+    import_module("virtool_workflow.analysis.skewer")
+    import_module("virtool_workflow.runtime.run_subprocess")
 
 
 def load_custom_fixtures():

{virtool_workflow-5.5.0a2.dist-info → virtool_workflow-6.0.0a1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 5.5.0a2
+Version: 6.0.0a1
 Summary: A framework for developing bioinformatics workflows for Virtool.
 Home-page: https://github.com/virtool/virtool-workflow
 License: MIT

{virtool_workflow-5.5.0a2.dist-info → virtool_workflow-6.0.0a1.dist-info}/RECORD

@@ -1,6 +1,6 @@
 virtool_workflow/__init__.py,sha256=Tw0lAFudpsFyCaiR2Oz_RKYU6N-mSCmhXDftm1WT37M,308
-virtool_workflow/analysis/__init__.py,sha256=2S-lxUMWzdlUykx79fkF9OChfH4BfFmDpQ8dp8Ix7Jo,126
-virtool_workflow/analysis/fastqc.py,sha256=qt-UnZZyyu5KaYJtuiRiaOsbzypZLba9I1V5jN2O300,12223
+virtool_workflow/analysis/__init__.py,sha256=eRMQhKOxijlFlYI78FzmHZoF1qYevBXycpIcmlrgFqI,57
+virtool_workflow/analysis/fastqc.py,sha256=iMIfJ1ZbGLnBjghumtMa5OoWE3D0eoX2uTp2ifbI7Zo,12160
 virtool_workflow/analysis/skewer.py,sha256=CemHLab4b_HIU1yHTB2CtHYRVM488pHnrggOxF90jAk,7159
 virtool_workflow/analysis/trimming.py,sha256=fTti5ND57Qcv5pIEKEZ9wYKe4K72-iYr6ixfnfJV60U,1457
 virtool_workflow/analysis/utils.py,sha256=YU1_yInZzTNl9nKQTebUz47kUEqZ__d0k-RMLX8DWOA,1108
@@ -24,7 +24,7 @@ virtool_workflow/files.py,sha256=hYztls3n30WTaI6rtZjrBobN1SaEGCHr4vWK8bhMJr0,384
 virtool_workflow/hooks.py,sha256=-KRoFfqR_nDLt3R0hC4Phmu7C-HCnfzd_obU_CyydBE,2689
 virtool_workflow/runtime/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 virtool_workflow/runtime/config.py,sha256=fHkprWxxqWeEWKOobxpVvSOS5Njk5Mq32sH-p5o_d8g,546
-virtool_workflow/runtime/discover.py,sha256=O4ToJ3Y7ToKs_Wuk3SqStaUHaAYRKt_FPew66YsKBEE,2784
+virtool_workflow/runtime/discover.py,sha256=IbCZ5FanxpGvdkdJJCgg22Ry9EhCIJbcVJQAToObLXk,2953
 virtool_workflow/runtime/events.py,sha256=ZIX3veBfC_2yNTdClHJaYMPn4KAF9JZqpQ3qDq4ox_E,138
 virtool_workflow/runtime/hook.py,sha256=b4IpkWQaGx2IjzDcxXzuv7ZnR7I_r4Dt2kOU_brNRm4,4354
 virtool_workflow/runtime/path.py,sha256=4-GpdpGeVKvyu_myLkW9mUT3AGsqYlBkGYB1RDZr2tI,562
@@ -35,8 +35,8 @@ virtool_workflow/runtime/run_subprocess.py,sha256=AviofEsOvp0buXRST-IxAW2txLwoTV
 virtool_workflow/runtime/sentry.py,sha256=6WNUYeQCoofP49cCmEy5bn_JRc3CSQmy7pnDW3XnAbc,748
 virtool_workflow/utils.py,sha256=wJHdTcuwC3wzYfJVM32MJo1Xdn-6r7V1bJRoLr9mhU0,520
 virtool_workflow/workflow.py,sha256=RxboCKLyCpfikPLIw7QFss77ERNlw8tJZhIXFB88DBs,2678
-virtool_workflow-5.5.0a2.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
-virtool_workflow-5.5.0a2.dist-info/METADATA,sha256=HaY5TrRKG9onHn4_Abqfx4a_o4YZZ_5fzJvRJiWaAvg,4321
-virtool_workflow-5.5.0a2.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-virtool_workflow-5.5.0a2.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
-virtool_workflow-5.5.0a2.dist-info/RECORD,,
+virtool_workflow-6.0.0a1.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
+virtool_workflow-6.0.0a1.dist-info/METADATA,sha256=t0F1dNKjC6FmjMnZV_akLeTEz2iuyYatyRdwV5yhG4E,4321
+virtool_workflow-6.0.0a1.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+virtool_workflow-6.0.0a1.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
+virtool_workflow-6.0.0a1.dist-info/RECORD,,