From dc8cd7dfbf33d3f85f5e6c442036dbe2097adcf5 Mon Sep 17 00:00:00 2001 From: Sebastian Diaz Date: Mon, 11 Dec 2023 15:34:13 +0100 Subject: [PATCH 1/2] 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 | 3 +++ cg/meta/workflow/mip_dna.py | 3 --- cg/meta/workflow/mip_rna.py | 4 ++++ 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/cg/meta/workflow/mip.py b/cg/meta/workflow/mip.py index 7bb0589c5a..5c6a3f2581 100644 --- a/cg/meta/workflow/mip.py +++ b/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) diff --git a/cg/meta/workflow/mip_dna.py b/cg/meta/workflow/mip_dna.py index 5f89f2765f..acca32dfb8 100644 --- a/cg/meta/workflow/mip_dna.py +++ b/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) diff --git a/cg/meta/workflow/mip_rna.py b/cg/meta/workflow/mip_rna.py index 22abbf6e76..90f938cb7e 100644 --- a/cg/meta/workflow/mip_rna.py +++ b/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) From e5c4f09cc42430893cd307070a36ee81756adfae Mon Sep 17 00:00:00 2001 From: Clinical Genomics Bot Date: Mon, 11 Dec 2023 14:34:43 +0000 Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=2054.2.0=20=E2=86=92=2054.2?= =?UTF-8?q?.1=20[skip=20ci]?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- cg/__init__.py | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index d69f167def..48aa093de9 100644 --- a/.bumpversion.cfg +++ b/.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} diff --git a/cg/__init__.py b/cg/__init__.py index 8ce4f8cf69..0bc83943cb 100644 --- a/cg/__init__.py +++ b/cg/__init__.py @@ -1,2 +1,2 @@ __title__ = "cg" -__version__ = "54.2.0" +__version__ = "54.2.1" diff --git a/pyproject.toml b/pyproject.toml index 7798aec396..20c5e4a640 100644 --- a/pyproject.toml +++ b/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 "] readme = "README.md"