Raredisease remove duplicate check (#4207)

### Changed
- Removed raredisease adapter content check from picardtools and WES depth threshold.

cg/constants/nf_analysis.py

@@ -28,9 +28,7 @@ class NfTowerStatus(StrEnum):
     "Contamination Status": {"norm": "eq", "threshold": "NO"},
     "adapter_cutting_adapter_trimmed_reads": {"norm": "lt", "threshold": None},
     "PCT_PF_UQ_READS_ALIGNED": {"norm": "gt", "threshold": 0.95},
-    "MEDIAN_TARGET_COVERAGE": {"norm": "gt", "threshold": 25},
     "PCT_TARGET_BASES_10X": {"norm": "gt", "threshold": 0.95},
-    "PCT_EXC_ADAPTER": {"norm": "lt", "threshold": 0.0005},
     "AT_DROPOUT": {"norm": "lt", "threshold": 10},
     "GC_DROPOUT": {"norm": "lt", "threshold": 10},
     RAREDISEASE_PREDICTED_SEX_METRIC: {"norm": "eq", "threshold": None},
@@ -44,7 +42,6 @@ class NfTowerStatus(StrEnum):
     "PCT_PF_UQ_READS_ALIGNED": {"norm": "gt", "threshold": 0.95},
     "MEDIAN_TARGET_COVERAGE": {"norm": "gt", "threshold": 25},
     "PCT_TARGET_BASES_10X": {"norm": "gt", "threshold": 0.95},
-    "PCT_EXC_ADAPTER": {"norm": "lt", "threshold": 0.0005},
     "AT_DROPOUT": {"norm": "lt", "threshold": 5},
     "GC_DROPOUT": {"norm": "lt", "threshold": 5},
     RAREDISEASE_PREDICTED_SEX_METRIC: {"norm": "eq", "threshold": None},

tests/fixtures/analysis/raredisease/raredisease_case_enough_reads_metrics_deliverables.yaml

@@ -321,9 +321,7 @@ metrics:
   name: PCT_EXC_DUPE
   step: multiqc
   value: 0.047463
-- condition:
-    norm: lt
-    threshold: 0.0005
+- condition: null
   header: null
   id: ADM1
   input: multiqc_data.json
@@ -1617,9 +1615,7 @@ metrics:
   name: PCT_EXC_DUPE
   step: multiqc
   value: 0.047463
-- condition:
-    norm: lt
-    threshold: 0.0005
+- condition: null
   header: null
   id: ADM2
   input: multiqc_data.json