Add rank model files for SNVs and SVs in deliverables

CONTRIBUTING.md

@@ -5,7 +5,7 @@ guidelines when contributing to Hermes.
 
 ## Deliverables Format
 
-Workflows must clearly define their deliverables in a [standardised format](https://atlas.scilifelab.se/infrastructure/dataflow/workflow/files_delivery/).
+Workflows must clearly define their deliverables in a [standardised format](https://atlas.scilifelab.se/infrastructure/data_management/dataflow/workflow/files_delivery/).
 
 ## Tags Format
 

cg_hermes/config/nallo.py

@@ -10,6 +10,7 @@
     AnalysisTags,
     BioinfoToolsTags,
     FamilyTags,
+    InputFileTags,
     MipTags,
     NalloTags,
     NextflowTags,
@@ -400,6 +401,16 @@
         "tags": [NextflowTags.SAMPLESHEET],
         "used_by": [UsageTags.CG, UsageTags.LONG_TERM_STORAGE],
     },
+    frozenset({"rank-model-snv"}): {
+        "is_mandatory": True,
+        "tags": [InputFileTags.RANK_MODEL_SNV],
+        "used_by": [UsageTags.SCOUT, UsageTags.LONG_TERM_STORAGE],
+    },
+    frozenset({"rank-model-sv"}): {
+        "is_mandatory": True,
+        "tags": [InputFileTags.RANK_MODEL_SV],
+        "used_by": [UsageTags.SCOUT, UsageTags.LONG_TERM_STORAGE],
+    },
 }
 
 NALLO_TAGS = {**NALLO_COMMON_TAGS, **NEXTFLOW_TAGS}

cg_hermes/config/raredisease.py

@@ -10,13 +10,14 @@
     AnalysisTags,
     BioinfoToolsTags,
     FamilyTags,
+    InputFileTags,
     MipTags,
     NextflowTags,
     QCTags,
     RarediseaseTags,
     ReportTags,
-    VariantTags,
     UsageTags,
+    VariantTags,
 )
 
 RAREDISEASE_COMMON_TAGS = {
@@ -344,6 +345,16 @@
         "is_mandatory": True,
         "used_by": [UsageTags.CLINICAL_DELIVERY, UsageTags.LONG_TERM_STORAGE],
     },
+    frozenset({"rank-model-snv"}): {
+        "is_mandatory": True,
+        "tags": [InputFileTags.RANK_MODEL_SNV],
+        "used_by": [UsageTags.SCOUT, UsageTags.LONG_TERM_STORAGE],
+    },
+    frozenset({"rank-model-sv"}): {
+        "is_mandatory": True,
+        "tags": [InputFileTags.RANK_MODEL_SV],
+        "used_by": [UsageTags.SCOUT, UsageTags.LONG_TERM_STORAGE],
+    },
 }
 
 RAREDISEASE_TAGS = {**RAREDISEASE_COMMON_TAGS, **NEXTFLOW_TAGS}

cg_hermes/constants/tags.py

@@ -518,6 +518,23 @@ def description(self) -> str:
         return descriptions.get(self, "Description not available")
 
 
+class InputFileTags(StrEnum):
+    RANK_MODEL_SNV = "rank-model-snv"
+    RANK_MODEL_SV = "rank-model-sv"
+
+    @classmethod
+    def name(cls) -> str:
+        return "Input File Tags"
+
+    @property
+    def description(self) -> str:
+        descriptions: dict[InputFileTags, str] = {
+            self.RANK_MODEL_SNV: "Rank model for SNV prioritization",
+            self.RANK_MODEL_SV: "Rank model for SV prioritization",
+        }
+        return descriptions.get(self, "Description not available")
+
+
 class MipTags(StrEnum):
     EXE_VER: str = "exe-ver"
     MIP_ANALYSE: str = "mip-analyse"
@@ -819,6 +836,7 @@ class UsageTags(StrEnum):
     AnalysisTags,
     BioinfoToolsTags,
     FamilyTags,
+    InputFileTags,
     QCTags,
     RawDataTags,
     ReportTags,

docs/raredisease_map.md

@@ -52,6 +52,8 @@
 | ped_check, peddy                                 | True        | peddy, ped-check                       | audit, scout, clinical-delivery                |
 | sex_check, peddy                                 | True        | peddy, sex-check                       | audit, scout, clinical-delivery                |
 | pedigree_fam, pedigree                           | True        | pedigree                               | scout                                          |
+| rank_model_snv, rank_and_filter                 | False       | rank-model-snv                         | scout                                          |
+| rank_model_sv, rank_and_filter                  | False       | rank-model-sv                          | scout                                          |
 | rhocallviz, annotate_snv                         | False       | rhocall-viz                            | scout                                          |
 | annotate_snv_mt, haplogrep                       | False       | haplogrep                              | scout, clinical-delivery                       |
 | chromograph_rhoviz, autozyg                      | False       | chromograph, autozyg                   | scout                                          |

tests/fixtures/nallo/case_id_deliverables.yaml

@@ -630,3 +630,13 @@ files:
   path: PATHTOCASE/CASEID_metrics_deliverables.yaml
   step: qc-metrics
   tag: qc-metrics
+- format: ini
+  id: CASEID
+  path: PATHTOCASE/grch38_rank_model_snvs_-v1.0-.ini
+  step: rank-model-snv
+  tag: rank-model-snv
+- format: ini
+  id: CASEID
+  path: PATHTOCASE/grch38_rank_model_svs_-v1.0-.ini
+  step: rank-model-sv
+  tag: rank-model-sv

tests/fixtures/raredisease/case_id_deliverables.yaml

@@ -830,3 +830,13 @@ files:
   path: PATHTOCASE/manifest.json
   step: manifest
   tag: manifest
+- format: ini
+  id: CASEID
+  path: PATHTOCASE/grch38_rank_model_-v0.4-.ini
+  step: rank-model-snv
+  tag: rank-model-snv
+- format: ini
+  id: CASEID
+  path: PATHTOCASE/grch38_sv_rank_model_-v0.2-.ini
+  step: rank-model-sv
+  tag: rank-model-sv