diff --git a/cg/meta/upload/scout/hk_tags.py b/cg/meta/upload/scout/hk_tags.py index ec9771825c..4e389ee8e6 100644 --- a/cg/meta/upload/scout/hk_tags.py +++ b/cg/meta/upload/scout/hk_tags.py @@ -12,6 +12,14 @@ class CaseTags(BaseModel): None, description="vcf_cancer_sv for rare disease and vcf_sv_cancer for cancer" ) sv_research_vcf: set[str] | None = Field(None, description="vcf_sv_research for rare disease") + vcf_snv: set[str] | None = Field( + None, description="vcf_snv for rare disease and vcf_cancer for cancer" + ) + vcf_snv_research: set[str] | None = Field(None, description="vcf_snv_research for rare disease") + vcf_sv: set[str] | None = Field( + None, description="vcf_cancer_sv for rare disease and vcf_sv_cancer for cancer" + ) + vcf_sv_research: set[str] | None = Field(None, description="vcf_sv_research for rare disease") vcf_str: set[str] = Field( None, description="Short Tandem Repeat variants, only for rare disease" ) @@ -21,6 +29,7 @@ class CaseTags(BaseModel): peddy_sex: set[str] | None = Field(None, description="Peddy sex check, only for rare disease") peddy_check: set[str] = Field(None, description="Peddy pedigree check, only for rare disease") multiqc_report: set[str] | None = Field(None, description="MultiQC report") + multiqc: set[str] | None = Field(None, description="MultiQC report") delivery_report: set[str] | None = Field(None, description="Delivery report") str_catalog: set[str] | None = Field( None, description="Variant catalog used with expansionhunter" diff --git a/cg/models/scout/scout_load_config.py b/cg/models/scout/scout_load_config.py index be53ab34c1..78990ad4dc 100644 --- a/cg/models/scout/scout_load_config.py +++ b/cg/models/scout/scout_load_config.py @@ -70,12 +70,12 @@ class ScoutMipIndividual(ScoutIndividual): class ScoutRarediseaseIndividual(ScoutIndividual): mt_bam: str | None = None bam_file: str | None = None - # chromograph_autozyg: str | None = None - # chromograph_coverage: str | None = None - # chromograph_regions: ChromographImages = ChromographImages() - # chromograph_sites: ChromographImages = ChromographImages() - # reviewer_alignment: Reviewer = Reviewer() - # reviewer_alignment_index: Reviewer = Reviewer() + chromograph_autozyg: str | None = None + chromograph_coverage: str | None = None + chromograph_regions: ChromographImages = ChromographImages() + chromograph_sites: ChromographImages = ChromographImages() + reviewer_alignment: Reviewer = Reviewer() + reviewer_alignment_index: Reviewer = Reviewer() rhocall_bed: str | None = None rhocall_wig: str | None = None tiddit_coverage_wig: str | None = None