fix most of teh tests

Author: diitaz93

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 +518,11 @@ 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"
+
+
 class MipTags(StrEnum):
     EXE_VER: str = "exe-ver"
     MIP_ANALYSE: str = "mip-analyse"
@@ -819,6 +824,7 @@ class UsageTags(StrEnum):
     AnalysisTags,
     BioinfoToolsTags,
     FamilyTags,
+    InputFileTags,
     QCTags,
     RawDataTags,
     ReportTags,

tests/fixtures/nallo/case_id_deliverables.yaml

@@ -633,10 +633,10 @@ files:
 - format: ini
   id: CASEID
   path: PATHTOCASE/CASEID_rank_model_snvs.ini
-  step: rank-models-snv
-  tag: rank-models-snv
+  step: rank-model-snv
+  tag: rank-model-snv
 - format: ini
   id: CASEID
   path: PATHTOCASE/CASEID_rank_model_svs.ini
-  step: rank-models-sv
-  tag: rank-models-sv
+  step: rank-model-sv
+  tag: rank-model-sv

tests/fixtures/raredisease/case_id_deliverables.yaml

@@ -833,10 +833,10 @@ files:
 - format: ini
   id: CASEID
   path: PATHTOCASE/CASEID_rank_model_snvs.ini
-  step: rank-models-snv
-  tag: rank-models-snv
+  step: rank-model-snv
+  tag: rank-model-snv
 - format: ini
   id: CASEID
   path: PATHTOCASE/CASEID_rank_model_svs.ini
-  step: rank-models-sv
-  tag: rank-models-sv
+  step: rank-model-sv
+  tag: rank-model-sv