Raredisease: add gene panel to workflow start (#3772)

### Added
- cg workflow raredisease config case forces gene panel generation

### Changed
- Allow hg19 as input for raredisease managed variants

cg/meta/workflow/raredisease.py

@@ -87,6 +87,11 @@ def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[l
         )
         return sample_sheet_entry.reformat_sample_content
 
+    @property
+    def is_gene_panel_required(self) -> bool:
+        """Return True if a gene panel is needs to be created using the information in StatusDB and exporting it from Scout."""
+        return True
+
     def get_target_bed(self, case_id: str, analysis_type: str) -> str:
         """
         Return the target bed file from LIMS and use default capture kit for WGS.
@@ -160,7 +165,9 @@ def write_managed_variants(self, case_id: str, content: list[str]) -> None:
 
     def get_managed_variants(self, case_id: str) -> list[str]:
         """Create and return the managed variants."""
-        return self._get_managed_variants(genome_build=self.get_genome_build(case_id=case_id))
+        return self._get_managed_variants(
+            genome_build=self.get_gene_panel_genome_build(case_id=case_id)
+        )
 
     def get_workflow_metrics(self, sample_id: str) -> dict:
         """Return Raredisease workflow metric conditions for a sample."""

tests/conftest.py

@@ -2499,6 +2499,12 @@ def raredisease_params_file_path(raredisease_dir, raredisease_case_id) -> Path:
     ).with_suffix(FileExtensions.YAML)
 
 
+@pytest.fixture(scope="function")
+def raredisease_gene_panel_path(raredisease_dir, raredisease_case_id) -> Path:
+    """Path to gene panel file."""
+    return Path(raredisease_dir, raredisease_case_id, "gene_panels").with_suffix(FileExtensions.BED)
+
+
 @pytest.fixture(scope="function")
 def raredisease_nexflow_config_file_path(raredisease_dir, raredisease_case_id) -> Path:
     """Path to config file."""
@@ -2601,6 +2607,7 @@ def raredisease_context(
         last_sequenced_at=datetime.now(),
         reads=total_sequenced_reads_pass,
         application_tag=wgs_application_tag,
+        reference_genome=GenomeVersion.HG19,
     )
 
     another_sample_enough_reads: Sample = helpers.add_sample(
@@ -2610,6 +2617,7 @@ def raredisease_context(
         last_sequenced_at=datetime.now(),
         reads=total_sequenced_reads_pass,
         application_tag=wgs_application_tag,
+        reference_genome=GenomeVersion.HG19,
     )
 
     helpers.add_relationship(
@@ -2638,6 +2646,7 @@ def raredisease_context(
         last_sequenced_at=datetime.now(),
         reads=total_sequenced_reads_not_pass,
         application_tag=wgs_application_tag,
+        reference_genome=GenomeVersion.HG19,
     )
 
     helpers.add_relationship(status_db, case=case_not_enough_reads, sample=sample_not_enough_reads)