virtool-workflow 5.5.0a1__py3-none-any.whl → 5.5.0a3__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/api/client.py

@@ -8,7 +8,7 @@ from virtool_workflow.api.utils import (
     raise_exception_by_status_code,
     decode_json_response,
 )
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.errors import JobsAPIError
 
 CHUNK_SIZE = 1024 * 1024 * 2

virtool_workflow/data/analyses.py

@@ -11,7 +11,7 @@ from virtool_core.models.reference import ReferenceNested
 from virtool_core.models.subtraction import SubtractionNested
 
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 
 
 class WFAnalysis:

virtool_workflow/data/indexes.py

@@ -12,7 +12,7 @@ from virtool_core.models.reference import ReferenceNested
 from virtool_core.utils import decompress_file
 
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.errors import MissingJobArgument
 
 

virtool_workflow/data/samples.py

@@ -11,7 +11,7 @@ from virtool_core.models.samples import Sample, Quality
 
 from virtool_workflow.analysis.utils import ReadPaths
 from virtool_workflow.api.client import APIClient
-from virtool_workflow.data.files import VirtoolFileFormat
+from virtool_workflow.files import VirtoolFileFormat
 from virtool_workflow.data.uploads import WFUploads
 from virtool_workflow.errors import JobsAPINotFound
 

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-5.5.0a1.dist-info → virtool_workflow-5.5.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: virtool-workflow
-Version: 5.5.0a1
+Version: 5.5.0a3
 Summary: A framework for developing bioinformatics workflows for Virtool.
 Home-page: https://github.com/virtool/virtool-workflow
 License: MIT

{virtool_workflow-5.5.0a1.dist-info → virtool_workflow-5.5.0a3.dist-info}/RECORD

@@ -1,30 +1,30 @@
 virtool_workflow/__init__.py,sha256=Tw0lAFudpsFyCaiR2Oz_RKYU6N-mSCmhXDftm1WT37M,308
-virtool_workflow/analysis/__init__.py,sha256=2S-lxUMWzdlUykx79fkF9OChfH4BfFmDpQ8dp8Ix7Jo,126
+virtool_workflow/analysis/__init__.py,sha256=eRMQhKOxijlFlYI78FzmHZoF1qYevBXycpIcmlrgFqI,57
 virtool_workflow/analysis/fastqc.py,sha256=qt-UnZZyyu5KaYJtuiRiaOsbzypZLba9I1V5jN2O300,12223
 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
 virtool_workflow/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 virtool_workflow/api/acquire.py,sha256=lViVFwQLf6IAmoK9kkzx3RAbXWgZ33KdYALDqK9eqGU,2139
-virtool_workflow/api/client.py,sha256=Y9BtSTXuXQh6GPYbndzsqCr-49fvGoZ7wnWUqAjEqao,4628
+virtool_workflow/api/client.py,sha256=OoAW6RdLBdnSJ0TMEtQq7SsbaLuGXTyJ0L2lzvfhV_E,4623
 virtool_workflow/api/utils.py,sha256=FNGD99UJKbQeNIxnoVwvsW1bXI25hRi87kpdiqsXkHE,3096
 virtool_workflow/cli.py,sha256=yEl1LziABKbjc5MCOoUGLy-iuqehOou37x9ox4LA92M,1441
 virtool_workflow/data/__init__.py,sha256=L2bQ5rMpnCMuLWDMwel4-wPchfQCTHH3EEwxDqwGOsY,610
-virtool_workflow/data/analyses.py,sha256=xJZEvQSOM7xIgkKRV3lh_u8LnFmwXZrq5ufnG92m7KU,3155
-virtool_workflow/data/files.py,sha256=hYztls3n30WTaI6rtZjrBobN1SaEGCHr4vWK8bhMJr0,384
+virtool_workflow/data/analyses.py,sha256=UdNrQWAvWHZwPLJinx_2_OK5eBeRlObVEx2QHcbFuRk,3150
 virtool_workflow/data/hmms.py,sha256=-ANZkM3C7p25zCEeS4WJFskBvHZWcpKjFDBZC2Z9HEA,3271
-virtool_workflow/data/indexes.py,sha256=BB-EtC11SnEE4mNiP-RJqQBc8btYuZqTkdRXyNMqXFw,8009
+virtool_workflow/data/indexes.py,sha256=xYBANmOT6Sr0GXWfw4WWNcxnITpnX3cKjj4zmu00jdg,8004
 virtool_workflow/data/jobs.py,sha256=LIKTX4jWm5cbNbdf9Foxmur0uf7_BeJY0aLT5Hr0Pp0,1669
 virtool_workflow/data/ml.py,sha256=Yoc4ePH-J_4BKi-wjCKFD6vuI58g3Jw7SKk4ri9ymQ4,1891
-virtool_workflow/data/samples.py,sha256=5qxUwgxqWCKXi3mxwIU2w_kRfEl4iQ64_PjEdIbgnK8,4701
+virtool_workflow/data/samples.py,sha256=tysGIGFssX4APlcQU52NIvjbtn6uX77ATLYS7Qhcgfg,4696
 virtool_workflow/data/subtractions.py,sha256=X-R8t5gIboHVE7kHyziWntuoyb1SbTjSV9UETB0Tt38,7282
 virtool_workflow/data/uploads.py,sha256=sIpuS2AtJ5yvZWitkzqb6hG1iLVe7K4q6UIsEDizFCE,899
 virtool_workflow/decorators.py,sha256=mh4_wBVLcAQYkn_aPonYEb2TP7NxORVdjBVgfehjHwQ,1285
 virtool_workflow/errors.py,sha256=CaFd4JNBAALU7ZK8_k9YJwluX_wUYZMbdf0uN7BsFXw,1215
+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-5.5.0a1.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
-virtool_workflow-5.5.0a1.dist-info/METADATA,sha256=h12KWupTQ2AzfipwSx0MT5rb5NChZsPdVW8C2Morfb4,4321
-virtool_workflow-5.5.0a1.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-virtool_workflow-5.5.0a1.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
-virtool_workflow-5.5.0a1.dist-info/RECORD,,
+virtool_workflow-5.5.0a3.dist-info/LICENSE,sha256=nkoVQw9W4aoQM9zgtNzHDmztap5TuXZ1L2-87vNr3w8,1097
+virtool_workflow-5.5.0a3.dist-info/METADATA,sha256=4V3gkWSiOMpoxzNa47sfj7TgyHdJ5z7KNsEMNBgHNVE,4321
+virtool_workflow-5.5.0a3.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+virtool_workflow-5.5.0a3.dist-info/entry_points.txt,sha256=d4MA8ZDTJOU0jKZ3ymtHZbfLVoRPgItEIN5U4uIqay8,62
+virtool_workflow-5.5.0a3.dist-info/RECORD,,