Add delivery report Raredisease (#3459)

### Added:
- Delivery report Raredisease

cg/cli/generate/report/utils.py

@@ -14,6 +14,7 @@
 from cg.meta.report.balsamic_qc import BalsamicQCReportAPI
 from cg.meta.report.balsamic_umi import BalsamicUmiReportAPI
 from cg.meta.report.mip_dna import MipDNAReportAPI
+from cg.meta.report.raredisease import RarediseaseReportAPI
 from cg.meta.report.report_api import ReportAPI
 from cg.meta.report.rnafusion import RnafusionReportAPI
 from cg.meta.report.taxprofiler import TaxprofilerReportAPI
@@ -22,6 +23,7 @@
 from cg.meta.workflow.balsamic_qc import BalsamicQCAnalysisAPI
 from cg.meta.workflow.balsamic_umi import BalsamicUmiAnalysisAPI
 from cg.meta.workflow.mip_dna import MipDNAAnalysisAPI
+from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
 from cg.meta.workflow.rnafusion import RnafusionAnalysisAPI
 from cg.meta.workflow.taxprofiler import TaxprofilerAnalysisAPI
 from cg.meta.workflow.tomte import TomteAnalysisAPI
@@ -98,6 +100,9 @@ def get_report_api_workflow(context: click.Context, workflow: Workflow) -> Repor
         Workflow.MIP_DNA: MipDNAReportAPI(
             config=context.obj, analysis_api=MipDNAAnalysisAPI(config=context.obj)
         ),
+        Workflow.RAREDISEASE: RarediseaseReportAPI(
+            config=context.obj, analysis_api=RarediseaseAnalysisAPI(config=context.obj)
+        ),
         Workflow.RNAFUSION: RnafusionReportAPI(
             config=context.obj, analysis_api=RnafusionAnalysisAPI(config=context.obj)
         ),

cg/cli/workflow/balsamic/options.py

@@ -13,8 +13,8 @@
 OPTION_GENOME_VERSION = click.option(
     "--genome-version",
     show_default=True,
-    default=GenomeVersion.hg19,
-    type=click.Choice([GenomeVersion.hg19, GenomeVersion.hg38, GenomeVersion.canfam3]),
+    default=GenomeVersion.HG19,
+    type=click.Choice([GenomeVersion.HG19, GenomeVersion.HG38, GenomeVersion.CANFAM3]),
     help="Type and build version of the reference genome. Set this option to override the default.",
 )
 OPTION_PANEL_BED = click.option(

cg/clients/chanjo2/models.py

@@ -38,3 +38,9 @@ def root_must_not_be_empty(cls, root: dict[str, CoverageMetrics]):
         if not root:
             raise ValueError("Coverage POST response must not be an empty dictionary")
         return root
+
+    def get_sample_coverage_metrics(self, sample_id: str) -> CoverageMetrics:
+        """Return the coverage metrics for the specified sample ID."""
+        if sample_id not in self.root:
+            raise ValueError(f"Sample ID '{sample_id}' not found in the coverage POST response")
+        return self.root[sample_id]

cg/constants/constants.py

@@ -165,9 +165,9 @@ class GenomeVersion(StrEnum):
     GRCh37: str = "GRCh37"
     GRCh38: str = "GRCh38"
     T2T_CHM13: str = "T2T-CHM13v2.0"
-    canfam3: str = "canfam3"
-    hg19: str = "hg19"
-    hg38: str = "hg38"
+    CANFAM3 = auto()
+    HG19 = auto()
+    HG38 = auto()
 
 
 class SampleType(StrEnum):

cg/constants/delivery.py

@@ -211,13 +211,17 @@
         "case_tags": RNAFUSION_ANALYSIS_CASE_TAGS,
         "sample_tags": RNAFUSION_ANALYSIS_SAMPLE_TAGS,
     },
+    Workflow.RAREDISEASE: {
+        "case_tags": NF_ANALYSIS_CASE_TAGS,
+        "sample_tags": NF_ANALYSIS_SAMPLE_TAGS,
+    },
     Workflow.TAXPROFILER: {
         "case_tags": NF_ANALYSIS_CASE_TAGS,
-        "sample_tags": NF_ANALYSIS_CASE_TAGS,
+        "sample_tags": NF_ANALYSIS_SAMPLE_TAGS,
     },
     Workflow.TOMTE: {
         "case_tags": NF_ANALYSIS_CASE_TAGS,
-        "sample_tags": NF_ANALYSIS_CASE_TAGS,
+        "sample_tags": NF_ANALYSIS_SAMPLE_TAGS,
     },
 }
 

cg/constants/nf_analysis.py

@@ -48,3 +48,7 @@ class NfTowerStatus(StrEnum):
     }
 }
 """
+
+RAREDISEASE_COVERAGE_FILE_TAGS: list[str] = ["coverage", "d4"]
+RAREDISEASE_COVERAGE_INTERVAL_TYPE: str = "genes"
+RAREDISEASE_COVERAGE_THRESHOLD: int = 10

cg/constants/report.py

@@ -22,6 +22,7 @@
     Workflow.BALSAMIC_QC,
     Workflow.BALSAMIC_UMI,
     Workflow.MIP_DNA,
+    Workflow.RAREDISEASE,
     Workflow.RNAFUSION,
     Workflow.TAXPROFILER,
     Workflow.TOMTE,
@@ -102,10 +103,12 @@
     "genome_build",
 ]
 
-REQUIRED_DATA_ANALYSIS_MIP_DNA_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_FIELDS + [
+REQUIRED_DATA_ANALYSIS_RAREDISEASE_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_FIELDS + [
     "panels",
 ]
 
+REQUIRED_DATA_ANALYSIS_MIP_DNA_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_RAREDISEASE_FIELDS
+
 REQUIRED_DATA_ANALYSIS_BALSAMIC_FIELDS: list[str] = REQUIRED_DATA_ANALYSIS_FIELDS + [
     "type",
     "variant_callers",
@@ -122,31 +125,31 @@
     "name",
     "id",
     "ticket",
-    "gender",
+    "sex",
     "source",
     "application",
     "methods",
     "metadata",
     "timestamps",
 ]
 
-_REQUIRED_SAMPLE_RARE_DISEASE_FIELDS: list[str] = _REQUIRED_SAMPLE_FIELDS + [
+REQUIRED_SAMPLE_RAREDISEASE_FIELDS: list[str] = _REQUIRED_SAMPLE_FIELDS + [
     "status",
 ]
 
 _REQUIRED_SAMPLE_CANCER_FIELDS: list[str] = _REQUIRED_SAMPLE_FIELDS + [
     "tumour",
 ]
 
-REQUIRED_SAMPLE_MIP_DNA_FIELDS: list[str] = _REQUIRED_SAMPLE_RARE_DISEASE_FIELDS
+REQUIRED_SAMPLE_MIP_DNA_FIELDS: list[str] = REQUIRED_SAMPLE_RAREDISEASE_FIELDS
 
 REQUIRED_SAMPLE_BALSAMIC_FIELDS: list[str] = _REQUIRED_SAMPLE_CANCER_FIELDS
 
 REQUIRED_SAMPLE_RNAFUSION_FIELDS: list[str] = _REQUIRED_SAMPLE_CANCER_FIELDS
 
 REQUIRED_SAMPLE_TAXPROFILER_FIELDS: list[str] = _REQUIRED_SAMPLE_FIELDS
 
-REQUIRED_SAMPLE_TOMTE_FIELDS: list[str] = _REQUIRED_SAMPLE_RARE_DISEASE_FIELDS
+REQUIRED_SAMPLE_TOMTE_FIELDS: list[str] = REQUIRED_SAMPLE_RAREDISEASE_FIELDS
 
 # Methods required fields (OPTIONAL: "library_prep", "sequencing")
 REQUIRED_SAMPLE_METHODS_FIELDS: list[str] = []
@@ -164,16 +167,25 @@
     "million_read_pairs",
 ]
 
-REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
-    "gender",
+REQUIRED_SAMPLE_METADATA_RAREDISEASE_WGS_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
+    "sex",
     "mapped_reads",
     "mean_target_coverage",
     "pct_10x",
 ]
 
-REQUIRED_SAMPLE_METADATA_MIP_DNA_FIELDS: list[str] = REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS + [
-    "bait_set",
-]
+REQUIRED_SAMPLE_METADATA_RAREDISEASE_FIELDS: list[str] = (
+    REQUIRED_SAMPLE_METADATA_RAREDISEASE_WGS_FIELDS
+    + [
+        "bait_set",
+    ]
+)
+
+REQUIRED_SAMPLE_METADATA_MIP_DNA_WGS_FIELDS: list[str] = (
+    REQUIRED_SAMPLE_METADATA_RAREDISEASE_WGS_FIELDS
+)
+
+REQUIRED_SAMPLE_METADATA_MIP_DNA_FIELDS: list[str] = REQUIRED_SAMPLE_METADATA_RAREDISEASE_FIELDS
 
 _REQUIRED_SAMPLE_METADATA_BALSAMIC_FIELDS: list[str] = _REQUIRED_SAMPLE_METADATA_FIELDS + [
     "mean_insert_size",

cg/constants/scout.py

@@ -1,9 +1,12 @@
-from enum import StrEnum
+from enum import StrEnum, auto
 
 from cg.constants import FileExtensions
 from cg.constants.housekeeper_tags import AlignmentFileTag
 
 
+HGNC_ID = "hgnc_id"
+
+
 class GenomeBuild(StrEnum):
     hg19: str = "37"
     hg38: str = "38"
@@ -29,7 +32,15 @@ class ScoutCustomCaseReportTags(StrEnum):
     GENE_FUSION_RESEARCH: str = "gene_fusion_research"
 
 
-MIP_CASE_TAGS = dict(
+class ScoutUploadKey(StrEnum):
+    SMN_TSV = auto()
+    SNV_VCF = auto()
+    SV_VCF = auto()
+    VCF_STR = auto()
+    VCF_FUSION = auto()
+
+
+RAREDISEASE_CASE_TAGS = dict(
     delivery_report={"delivery-report"},
     multiqc_report={"multiqc-html"},
     peddy_check={"ped-check", "peddy"},
@@ -46,6 +57,8 @@ class ScoutCustomCaseReportTags(StrEnum):
     vcf_str={"vcf-str"},
 )
 
+MIP_CASE_TAGS: dict[str, set[str]] = RAREDISEASE_CASE_TAGS
+
 BALSAMIC_CASE_TAGS = dict(
     sv_vcf={"vcf-sv-clinical"},
     snv_vcf={"vcf-snv-clinical"},
@@ -74,7 +87,7 @@ class ScoutCustomCaseReportTags(StrEnum):
     vcf_fusion={"vcf-fusion"},
 )
 
-MIP_SAMPLE_TAGS = dict(
+RAREDISEASE_SAMPLE_TAGS = dict(
     bam_file={"bam"},
     alignment_file={"cram"},
     vcf2cytosure={"vcf2cytosure"},
@@ -89,6 +102,8 @@ class ScoutCustomCaseReportTags(StrEnum):
     mitodel_file={"mitodel"},
 )
 
+MIP_SAMPLE_TAGS: dict[str, set[str]] = RAREDISEASE_SAMPLE_TAGS
+
 BALSAMIC_SAMPLE_TAGS = dict(
     bam_file={"bam"},
     alignment_file={"cram"},

cg/meta/report/balsamic.py

@@ -18,7 +18,7 @@
     Workflow,
 )
 from cg.constants.constants import AnalysisType
-from cg.constants.scout import BALSAMIC_CASE_TAGS
+from cg.constants.scout import ScoutUploadKey
 from cg.meta.report.field_validators import get_million_read_pairs
 from cg.meta.report.report_api import ReportAPI
 from cg.meta.workflow.balsamic import BalsamicAnalysisAPI
@@ -33,7 +33,7 @@
     BalsamicTargetedSampleMetadataModel,
     BalsamicWGSSampleMetadataModel,
 )
-from cg.models.report.report import CaseModel, ScoutReportFiles
+from cg.models.report.report import CaseModel, ScoutReportFiles, ReportRequiredFields
 from cg.models.report.sample import SampleModel
 from cg.store.models import Bed, BedVersion, Case, Sample
 
@@ -139,8 +139,12 @@ def is_report_accredited(
     def get_scout_uploaded_files(self, case_id: str) -> ScoutReportFiles:
         """Return files that will be uploaded to Scout."""
         return ScoutReportFiles(
-            snv_vcf=self.get_scout_uploaded_file_from_hk(case_id=case_id, scout_tag="snv_vcf"),
-            sv_vcf=self.get_scout_uploaded_file_from_hk(case_id=case_id, scout_tag="sv_vcf"),
+            snv_vcf=self.get_scout_uploaded_file_from_hk(
+                case_id=case_id, scout_key=ScoutUploadKey.SNV_VCF
+            ),
+            sv_vcf=self.get_scout_uploaded_file_from_hk(
+                case_id=case_id, scout_key=ScoutUploadKey.SV_VCF
+            ),
         )
 
     def get_required_fields(self, case: CaseModel) -> dict:
@@ -167,28 +171,26 @@ def get_required_fields(self, case: CaseModel) -> dict:
             required_sample_metadata_fields: list[str] = (
                 REQUIRED_SAMPLE_METADATA_BALSAMIC_TARGETED_FIELDS
             )
-        return {
-            "report": REQUIRED_REPORT_FIELDS,
-            "customer": REQUIRED_CUSTOMER_FIELDS,
-            "case": REQUIRED_CASE_FIELDS,
-            "applications": self.get_application_required_fields(
+
+        report_required_fields = ReportRequiredFields(
+            applications=self.get_application_required_fields(
                 case=case, required_fields=REQUIRED_APPLICATION_FIELDS
             ),
-            "data_analysis": required_data_analysis_fields,
-            "samples": self.get_sample_required_fields(
-                case=case, required_fields=REQUIRED_SAMPLE_BALSAMIC_FIELDS
+            case=REQUIRED_CASE_FIELDS,
+            customer=REQUIRED_CUSTOMER_FIELDS,
+            data_analysis=required_data_analysis_fields,
+            metadata=self.get_sample_required_fields(
+                case=case, required_fields=required_sample_metadata_fields
             ),
-            "methods": self.get_sample_required_fields(
+            methods=self.get_sample_required_fields(
                 case=case, required_fields=REQUIRED_SAMPLE_METHODS_FIELDS
             ),
-            "timestamps": self.get_timestamp_required_fields(
-                case=case, required_fields=REQUIRED_SAMPLE_TIMESTAMP_FIELDS
+            report=REQUIRED_REPORT_FIELDS,
+            samples=self.get_sample_required_fields(
+                case=case, required_fields=REQUIRED_SAMPLE_BALSAMIC_FIELDS
             ),
-            "metadata": self.get_sample_required_fields(
-                case=case, required_fields=required_sample_metadata_fields
+            timestamps=self.get_timestamp_required_fields(
+                case=case, required_fields=REQUIRED_SAMPLE_TIMESTAMP_FIELDS
             ),
-        }
-
-    def get_upload_case_tags(self) -> dict:
-        """Return Balsamic upload case tags."""
-        return BALSAMIC_CASE_TAGS
+        )
+        return report_required_fields.model_dump()

cg/meta/report/balsamic_umi.py

@@ -1,6 +1,5 @@
 import logging
 
-from cg.constants.scout import BALSAMIC_UMI_CASE_TAGS
 from cg.meta.report.balsamic import BalsamicReportAPI
 from cg.meta.workflow.balsamic_umi import BalsamicUmiAnalysisAPI
 from cg.models.cg_config import CGConfig
@@ -14,7 +13,3 @@ class BalsamicUmiReportAPI(BalsamicReportAPI):
     def __init__(self, config: CGConfig, analysis_api: BalsamicUmiAnalysisAPI):
         super().__init__(config=config, analysis_api=analysis_api)
         self.analysis_api: BalsamicUmiAnalysisAPI = analysis_api
-
-    def get_upload_case_tags(self) -> dict:
-        """Return Balsamic UMI upload case tags."""
-        return BALSAMIC_UMI_CASE_TAGS