Merge pull request #1842 from milaboratory/mixcr-regression-tests/bru…

…ker_v2 Regression tests changes in the bruker_v2
milaboratory · Oct 31, 2024 · 75d461b · 75d461b
2 parents 45e680f + 2eda969
commit 75d461b
Showing 1 changed file with 65 additions and 75 deletions.
diff --git a/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml b/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml
@@ -15,8 +15,8 @@ mitool:
     pattern: "^(CELL:N{10})ggg\\^(R2:*)"
     unstranded: false
     maxErrorBudget: 10.0
-    trimmingQualityThreshold: null
-    trimmingWindowSize: null
+    trimmingQualityThreshold: 20
+    trimmingWindowSize: 5
     replaceWildcards: true
     splitBySample: true
   refineTags:
@@ -46,78 +46,42 @@ mitool:
       maxTotalErrors: 3
       postFilter: null
   consensus:
-    - parameters:
-        aAssemblerParameters:
-          bandWidth: 4
-          scoring:
-            type: linear
-            alphabet: nucleotide
-            subsMatrix: "simple(match = 5, mismatch = -4)"
-            gapPenalty: -19
-          minAlignmentScore: 80
-          maxNormalizedAlignmentPenalty: 0.13
-          trimMinimalSumQuality: 0
-          trimReferenceRegion: true
-          maxQuality: 45
-        kMapParameters:
-          k: 9
-          useQ1Score: true
-          coreSequenceKMers: 20
-          coreSequenceRecordScore: 20
-          neighbourhoodSize: 2
-        positiveMinQualityShare: 0.13
-        positiveMinIntersectionQuality: 150
-        minAlignmentScoreForDiscardRecord: 0
-        maxNormalizedAlignmentPenaltyForDiscardRecord: 0.0
-        minRecordSharePerConsensus: 0.001
-        minRecordsPerConsensus: 3
-        useWeightsForRecordsPerConsensus: true
-        minRecordWeightForUse: 0
-        maxIterationsPerConsensus: 8
-        maxConsensuses: 0
-      groupingTagTypes:
-        - Cell
-      payloadTagTypes:
-        - Targets
-      saveUnusedReads: true
-      saveDiscardedReads: true
-      inferMinRecordsPerConsensus: true
-    - parameters:
-        aAssemblerParameters:
-          bandWidth: 4
-          scoring:
-            type: linear
-            alphabet: nucleotide
-            subsMatrix: "simple(match = 5, mismatch = -4)"
-            gapPenalty: -19
-          minAlignmentScore: 71
-          maxNormalizedAlignmentPenalty: 0.1
-          trimMinimalSumQuality: 0
-          trimReferenceRegion: true
-          maxQuality: 45
-        kMapParameters:
-          k: 9
-          useQ1Score: true
-          coreSequenceKMers: 20
-          coreSequenceRecordScore: 20
-          neighbourhoodSize: 2
-        positiveMinQualityShare: 0.14
-        positiveMinIntersectionQuality: 239
-        minAlignmentScoreForDiscardRecord: 0
-        maxNormalizedAlignmentPenaltyForDiscardRecord: 0.0
-        minRecordSharePerConsensus: 1.0
-        minRecordsPerConsensus: 3
-        useWeightsForRecordsPerConsensus: true
-        minRecordWeightForUse: 0
-        maxIterationsPerConsensus: 8
-        maxConsensuses: 0
-      groupingTagTypes:
-        - Cell
-      payloadTagTypes:
-        - Targets
-      saveUnusedReads: true
-      saveDiscardedReads: true
-      inferMinRecordsPerConsensus: true
+    parameters:
+      aAssemblerParameters:
+        bandWidth: 4
+        scoring:
+          type: linear
+          alphabet: nucleotide
+          subsMatrix: "simple(match = 5, mismatch = -10)"
+          gapPenalty: -19
+        minAlignmentScore: 62
+        maxNormalizedAlignmentPenalty: 0.4
+        trimMinimalSumQuality: 0
+        trimReferenceRegion: true
+        maxQuality: 45
+      kMapParameters:
+        k: 9
+        useQ1Score: true
+        coreSequenceKMers: 20
+        coreSequenceRecordScore: 20
+        neighbourhoodSize: 2
+      positiveMinQualityShare: 0.21
+      positiveMinIntersectionQuality: 238
+      minAlignmentScoreForDiscardRecord: 0
+      maxNormalizedAlignmentPenaltyForDiscardRecord: 0.0
+      minRecordSharePerConsensus: 0.01
+      minRecordsPerConsensus: 0
+      useWeightsForRecordsPerConsensus: false
+      minRecordWeightForUse: 0
+      maxIterationsPerConsensus: 90
+      maxConsensuses: 0
+    groupingTagTypes:
+      - Cell
+    payloadTagTypes:
+      - Targets
+    saveUnusedReads: false
+    saveDiscardedReads: false
+    inferMinRecordsPerConsensus: false
 align:
   species: ""
   libraryName: default
@@ -429,7 +393,33 @@ assemble:
     maxBadPointsPercent: 0.7
     mappingThreshold: 2of5
     minimalQuality: 0
-    postFilters: null
+    postFilters:
+      - type: filter_in_groups
+        isolationKeys:
+          - geneLabel:ReliableChain
+          - allTags:Cell
+        nestedFilter:
+          type: filter_groups
+          groupingKeys:
+            - clone
+          predicates:
+            - metrics:
+                - type: group_metric_sum_weight
+                  reportHist: null
+              operator:
+                type: group_operator_cumtop
+                share: 0.9
+                accept: High
+              expectedSorting: []
+              requiredSequences: []
+          expectedSorting:
+            - clone
+          requiredSequences: []
+        aggregateReport: true
+        expectedSorting:
+          - geneLabel:ReliableChain
+          - allTags:Cell
+          - clone
   inferMinRecordsPerConsensus: false
 assembleContigs:
   ignoreTags: false