Added method get_managed_variants to mip rna workflow (#2757)(patch)

The `MipRNAAnalysisAPI` didn't have a `get_managed_variants` method which raised an error when running `cg workflow mip-rna start -sa star_fusion hugewasp`

### Added

- Method `get_managed_variants` to `MipRNAAnalysisAPI`

### Changed

- Moved method `write_managed_variants` from `MipDNAAnalysisAPI` to `MipAnalysisAPI` so that it is available also for MipRNA

cg/meta/workflow/mip.py

@@ -329,3 +329,6 @@ def get_pipeline_version(self, case_id: str) -> str:
         )
         sample_info: MipBaseSampleInfo = MipBaseSampleInfo(**sample_info_raw)
         return sample_info.mip_version
+
+    def write_managed_variants(self, case_id: str, content: list[str]) -> None:
+        self._write_managed_variants(out_dir=Path(self.root, case_id), content=content)

cg/meta/workflow/mip_dna.py

@@ -73,6 +73,3 @@ def get_gene_panel(self, case_id: str) -> list[str]:
     def get_managed_variants(self) -> list[str]:
         """Create and return the managed variants."""
         return self._get_managed_variants(genome_build=GENOME_BUILD_37)
-
-    def write_managed_variants(self, case_id: str, content: list[str]) -> None:
-        self._write_managed_variants(out_dir=Path(self.root, case_id), content=content)

cg/meta/workflow/mip_rna.py

@@ -56,3 +56,7 @@ def config_sample(self, link_obj, panel_bed: str | None = None) -> dict[str, str
     def get_gene_panel(self, case_id: str) -> list[str]:
         """Create and return the aggregated gene panel file."""
         return self._get_gene_panel(case_id=case_id, genome_build=GENOME_BUILD_38)
+
+    def get_managed_variants(self) -> list[str]:
+        """Create and return the managed variants."""
+        return self._get_managed_variants(genome_build=GENOME_BUILD_38)