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milaboratory · Oct 31, 2024 · 6e5e0a7 · 6e5e0a7
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commit 6e5e0a7
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Showing 2 changed files with 52 additions and 52 deletions.
diff --git a/src/main/resources/presets/blocks/mitool.yaml b/src/main/resources/presets/blocks/mitool.yaml
@@ -2,38 +2,38 @@ mitool-consensus-1-steps:
   abstract: true
   mitool:
     consensus:
-      - parameters:
-          aAssemblerParameters:
-            bandWidth: 4
-            scoring:
-              type: linear
-              alphabet: nucleotide
-              subsMatrix: "simple(match = 5, mismatch = -4)"
-              gapPenalty: -19
-            minAlignmentScore: 300
-            maxNormalizedAlignmentPenalty: 0.30
-            trimMinimalSumQuality: 0
-            trimReferenceRegion: true
-            maxQuality: 45
-          kMapParameters:
-            k: 9
-            useQ1Score: true
-            coreSequenceKMers: 20
-            coreSequenceRecordScore: 20
-            neighbourhoodSize: 2
-          positiveMinQualityShare: 0.2
-          positiveMinIntersectionQuality: 300
-          minAlignmentScoreForDiscardRecord: 0
-          maxNormalizedAlignmentPenaltyForDiscardRecord: 0.0
-          minRecordSharePerConsensus: 0.001
-          minRecordsPerConsensus: 3
-          useWeightsForRecordsPerConsensus: true
-          minRecordWeightForUse: 0
-          maxIterationsPerConsensus: 8
-          maxConsensuses: 0
-        saveUnusedReads: true
-        saveDiscardedReads: true
-        inferMinRecordsPerConsensus: true
+      parameters:
+        aAssemblerParameters:
+          bandWidth: 4
+          scoring:
+            type: linear
+            alphabet: nucleotide
+            subsMatrix: "simple(match = 5, mismatch = -4)"
+            gapPenalty: -19
+          minAlignmentScore: 300
+          maxNormalizedAlignmentPenalty: 0.30
+          trimMinimalSumQuality: 0
+          trimReferenceRegion: true
+          maxQuality: 45
+        kMapParameters:
+          k: 9
+          useQ1Score: true
+          coreSequenceKMers: 20
+          coreSequenceRecordScore: 20
+          neighbourhoodSize: 2
+        positiveMinQualityShare: 0.2
+        positiveMinIntersectionQuality: 300
+        minAlignmentScoreForDiscardRecord: 0
+        maxNormalizedAlignmentPenaltyForDiscardRecord: 0.0
+        minRecordSharePerConsensus: 0.001
+        minRecordsPerConsensus: 3
+        useWeightsForRecordsPerConsensus: true
+        minRecordWeightForUse: 0
+        maxIterationsPerConsensus: 8
+        maxConsensuses: 0
+      saveUnusedReads: true
+      saveDiscardedReads: true
+      inferMinRecordsPerConsensus: true
 
 mitool-consensus-2-steps:
   abstract: true

diff --git a/src/main/resources/presets/protocols/bruker.yaml b/src/main/resources/presets/protocols/bruker.yaml
@@ -49,26 +49,26 @@
     consensus:
       inheritFrom: mitool-consensus-1-steps
       overrides:
-        - groupingTagTypes:
-            - Cell
-          payloadTagTypes:
-            - Targets
-          parameters:
-            maxIterationsPerConsensus: 90
-            useWeightsForRecordsPerConsensus: false
-            aAssemblerParameters:
-              bandWidth: 4
-              scoring:
-                alphabet: nucleotide
-                subsMatrix: "simple(match = 5, mismatch = -10)"
-                gapPenalty: -19
-              minAlignmentScore: 60
-              maxNormalizedAlignmentPenalty: 0.4
-            positiveMinQualityShare: 0.21
-            positiveMinIntersectionQuality: 238
-            minRecordSharePerConsensus: 0.01
-            minRecordsPerConsensus: 0
-            maxConsensuses: 0
+        groupingTagTypes:
+          - Cell
+        payloadTagTypes:
+          - Targets
+        parameters:
+          maxIterationsPerConsensus: 90
+          useWeightsForRecordsPerConsensus: false
+          aAssemblerParameters:
+            bandWidth: 4
+            scoring:
+              alphabet: nucleotide
+              subsMatrix: "simple(match = 5, mismatch = -10)"
+              gapPenalty: -19
+            minAlignmentScore: 60
+            maxNormalizedAlignmentPenalty: 0.4
+          positiveMinQualityShare: 0.21
+          positiveMinIntersectionQuality: 238
+          minRecordSharePerConsensus: 0.01
+          minRecordsPerConsensus: 0
+          maxConsensuses: 0
   align:
     inheritFrom: align-single-cell
     overrides: