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Added method get_managed_variants to mip rna workflow #2757

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merged 2 commits into from
Dec 11, 2023
Merged

Added method get_managed_variants to mip rna workflow #2757

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d5b70a3
Added method get_managed_variants to mip rna workflow
diitaz93 Dec 11, 2023
34ced58
Move write_managed_variants to base mip API
diitaz93 Dec 11, 2023
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3 changes: 3 additions & 0 deletions cg/meta/workflow/mip.py
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Expand Up @@ -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)
3 changes: 0 additions & 3 deletions cg/meta/workflow/mip_dna.py
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Expand Up @@ -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)
4 changes: 4 additions & 0 deletions cg/meta/workflow/mip_rna.py
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Expand Up @@ -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)
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