DEV - Switch reference genome to hg38 for raredisease

README.md

@@ -63,4 +63,7 @@ For development, use `poetry install --all-extras` to install development depend
 [codefactor-badge]: https://www.codefactor.io/repository/github/clinical-genomics/cg/badge
 [codefactor-url]: https://www.codefactor.io/repository/github/clinical-genomics/cg
 [black-image]: https://img.shields.io/badge/code%20style-black-000000.svg
-[black-url]: https://github.com/psf/black
+[black-url]: https://github.com/psf/black
+
+Old codes find the light, Newer maps trace hidden flaws, Healing with data.
+

cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/raredisease.py

@@ -24,7 +24,6 @@
 
 
 class RarediseaseParamsFileCreator(ParamsFileCreator):
-
     def __init__(self, store: Store, lims: LimsAPI, params: str):
         super().__init__(params)
         self.store = store
@@ -91,7 +90,7 @@ def _get_target_bed_from_lims(self, case_id: str) -> str:
         if target_bed_shortname:
             bed_version: BedVersion = (
                 self.store.get_bed_version_by_short_name_and_genome_version_strict(
-                    short_name=target_bed_shortname, genome_version=BedVersionGenomeVersion.HG19
+                    short_name=target_bed_shortname, genome_version=BedVersionGenomeVersion.HG38
                 )
             )
             return bed_version.filename

cg/services/analysis_starter/configurator/file_creators/nextflow/utils.py

@@ -7,7 +7,7 @@ def get_genome_build(workflow: Workflow) -> GenePanelGenomeBuild | None:
     workflow_to_genome_build: dict[Workflow, GenePanelGenomeBuild] = {
         Workflow.MIP_DNA: GenePanelGenomeBuild.hg19,
         Workflow.NALLO: GenePanelGenomeBuild.hg38,
-        Workflow.RAREDISEASE: GenePanelGenomeBuild.hg19,
+        Workflow.RAREDISEASE: GenePanelGenomeBuild.hg38,
         Workflow.TOMTE: GenePanelGenomeBuild.hg38,
     }
     return workflow_to_genome_build.get(workflow)

cg/services/analysis_starter/factories/configurator_factory.py

@@ -211,7 +211,7 @@ def _get_managed_variants_file_creator(self, workflow: Workflow) -> ManagedVaria
     def _get_scout_api(self, workflow: Workflow) -> ScoutAPI:
         return (
             self.cg_config.scout_api_38
-            if workflow == Workflow.NALLO
+            if workflow in [Workflow.NALLO, Workflow.RAREDISEASE]
             else self.cg_config.scout_api_37
         )
 

tests/services/analysis_starter/file_creators/params_file/test_params_file_creator.py

@@ -51,7 +51,7 @@ def test_raredisease_params_file_creator(
         lambda short_name, genome_version: (
             create_autospec(BedVersion, filename="bed_version.bed")
             if short_name == "target_bed_shortname_123"
-            and genome_version == BedVersionGenomeVersion.HG19
+            and genome_version == BedVersionGenomeVersion.HG38
             else create_autospec(BedVersion)
         )
     )

tests/services/analysis_starter/file_creators/test_gene_panel_file_creator.py

@@ -223,7 +223,7 @@ def test_add_gene_panels_in_combo(
     "case_id, expected_genome_build",
     [
         (MIP_DNA_CASE_ID, GenePanelGenomeBuild.hg19),
-        (RAREDISEASE_CASE_ID, GenePanelGenomeBuild.hg19),
+        (RAREDISEASE_CASE_ID, GenePanelGenomeBuild.hg38),
         (NALLO_CASE_ID, GenePanelGenomeBuild.hg38),
         (TOMTE_CASE_ID, GenePanelGenomeBuild.hg38),
     ],

tests/services/analysis_starter/test_configurator_factory.py

@@ -82,8 +82,6 @@ def test_get_microsalt_configurator(cg_context: CGConfig):
 @pytest.mark.parametrize(
     "workflow, pipeline_extension_class",
     [
-        (Workflow.NALLO, NalloExtension),
-        (Workflow.RAREDISEASE, RarediseaseExtension),
         (Workflow.RNAFUSION, PipelineExtension),
         (Workflow.TAXPROFILER, PipelineExtension),
         (Workflow.TOMTE, TomteExtension),
@@ -109,6 +107,50 @@ def test_nextflow_configurator_factory_success(
     assert isinstance(configurator.pipeline_extension, pipeline_extension_class)
 
 
+def test_nextflow_configurator_factory_raredisease_success(
+    cg_context: CGConfig,
+):
+    # GIVEN a configurator factory
+    configurator_factory = ConfiguratorFactory(cg_config=cg_context)
+
+    # WHEN getting the configurator for the workflow
+    configurator = cast(
+        NextflowConfigurator, configurator_factory.get_configurator(Workflow.RAREDISEASE)
+    )
+
+    # THEN the configurator is of the expected type
+    assert isinstance(configurator, NextflowConfigurator)
+    assert isinstance(configurator.params_file_creator, ParamsFileCreator)
+    assert isinstance(configurator.sample_sheet_creator, SampleSheetCreator)
+    assert isinstance(configurator.pipeline_extension, RarediseaseExtension)
+    assert (
+        configurator.pipeline_extension.gene_panel_file_creator.scout_api == cg_context.scout_api_38
+    )
+    assert (
+        configurator.pipeline_extension.managed_variants_file_creator.scout_api
+        == cg_context.scout_api_38
+    )
+
+
+def test_nextflow_configurator_factory_nallo_success(
+    cg_context: CGConfig,
+):
+    # GIVEN a configurator factory
+    configurator_factory = ConfiguratorFactory(cg_config=cg_context)
+
+    # WHEN getting the configurator for the workflow
+    configurator = cast(NextflowConfigurator, configurator_factory.get_configurator(Workflow.NALLO))
+
+    # THEN the configurator is of the expected type
+    assert isinstance(configurator, NextflowConfigurator)
+    assert isinstance(configurator.params_file_creator, ParamsFileCreator)
+    assert isinstance(configurator.sample_sheet_creator, SampleSheetCreator)
+    assert isinstance(configurator.pipeline_extension, NalloExtension)
+    assert (
+        configurator.pipeline_extension.gene_panel_file_creator.scout_api == cg_context.scout_api_38
+    )
+
+
 def test_get_mip_dna_configurator():
     # GIVEN a MIP-DNA config
     mip_config: MipConfig = create_autospec(