Merge branch 'master' into metrics-deliver

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 54.2.0
+current_version = 54.2.1
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "54.2.0"
+__version__ = "54.2.1"

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)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "54.2.0"
+version = "54.2.1"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"