add scout keywords to constructor

Clinical-Genomics · Sep 3, 2024 · d7e4525 · d7e4525
1 parent 57d9b61
commit d7e4525
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Showing 2 changed files with 15 additions and 6 deletions.
diff --git 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
@@ -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