diff --git a/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml b/regression/presets/analyze/bruker-sc-xcr-vdj-beacon.yaml index 19177819a..0934fd906 100644 --- 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