Regression tests changes in the rna-seq-with-umi-preset

regression/presets/analyze/rna-seq-with-umi.yaml

@@ -0,0 +1,389 @@
+flags:
+ - species
+ - tagPattern
+ - materialType
+pipeline:
+ - align
+ - refineTagsAndSort
+ - assemblePartial
+ - assemblePartial
+ - extend
+ - assemble
+ - assembleContigs
+ - exportClones
+align:
+ species: ""
+ libraryName: default
+ trimmingQualityThreshold: 10
+ trimmingWindowSize: 6
+ chains: ALL
+ replaceWildcards: true
+ overlapPairedReads: true
+ bamDropNonVDJ: false
+ writeFailedAlignments: false
+ tagPattern: null
+ tagUnstranded: false
+ tagMaxBudget: 10.0
+ headerExtractors: []
+ readIdAsCellTag: false
+ sampleTable: null
+ tagsValidations:
+ - type: MustContainTagType
+ tagType: Cell
+ - type: MustContainTagType
+ tagType: Molecule
+ splitBySample: true
+ limit: null
+ parameters:
+ vParameters:
+ geneFeatureToAlign: VTranscriptWithP
+ minSumScore: 60
+ relativeMinScore: 0.97
+ maxHits: 5
+ edgeRealignmentMinScoreOverride: 35
+ parameters:
+ type: kaligner2
+ mapperNValue: 9
+ mapperKValue: 1
+ floatingLeftBound: false
+ floatingRightBound: true
+ mapperAbsoluteMinClusterScore: 250
+ mapperExtraClusterScore: -38
+ mapperMatchScore: 127
+ mapperMismatchScore: -14
+ mapperOffsetShiftScore: -82
+ mapperSlotCount: 6
+ mapperMaxClusters: 15
+ mapperMaxClusterIndels: 4
+ mapperKMersPerPosition: 4
+ mapperAbsoluteMinScore: 250
+ mapperRelativeMinScore: 0.75
+ mapperMinSeedsDistance: 6
+ mapperMaxSeedsDistance: 6
+ alignmentStopPenalty: 0
+ absoluteMinScore: 150
+ relativeMinScore: 0.8
+ maxHits: 3
+ scoring:
+ type: affine
+ alphabet: nucleotide
+ subsMatrix: "simple(match = 10, mismatch = -19)"
+ gapOpenPenalty: -62
+ gapExtensionPenalty: -11
+ dParameters:
+ geneFeatureToAlign: DRegionWithP
+ relativeMinScore: 0.85
+ absoluteMinScore: 25.0
+ maxHits: 3
+ scoring:
+ type: linear
+ alphabet: nucleotide
+ subsMatrix: "simple(match = 5, mismatch = -9)"
+ gapPenalty: -12
+ jParameters:
+ geneFeatureToAlign: JRegionWithP
+ minSumScore: 150
+ relativeMinScore: 0.97
+ maxHits: 5
+ parameters:
+ type: kaligner2
+ mapperNValue: 8
+ mapperKValue: 1
+ floatingLeftBound: true
+ floatingRightBound: false
+ mapperAbsoluteMinClusterScore: 102
+ mapperExtraClusterScore: -38
+ mapperMatchScore: 95
+ mapperMismatchScore: -14
+ mapperOffsetShiftScore: -82
+ mapperSlotCount: 6
+ mapperMaxClusters: 4
+ mapperMaxClusterIndels: 4
+ mapperKMersPerPosition: 4
+ mapperAbsoluteMinScore: 100
+ mapperRelativeMinScore: 0.8
+ mapperMinSeedsDistance: 5
+ mapperMaxSeedsDistance: 5
+ alignmentStopPenalty: 0
+ absoluteMinScore: 150
+ relativeMinScore: 0.8
+ maxHits: 3
+ scoring:
+ type: affine
+ alphabet: nucleotide
+ subsMatrix: "simple(match = 10, mismatch = -19)"
+ gapOpenPenalty: -62
+ gapExtensionPenalty: -11
+ cParameters:
+ geneFeatureToAlign: CExon1
+ minSumScore: 40
+ relativeMinScore: 0.97
+ maxHits: 5
+ parameters:
+ type: kaligner
+ mapperKValue: 5
+ floatingLeftBound: false
+ floatingRightBound: false
+ mapperAbsoluteMinScore: 95.0
+ mapperRelativeMinScore: 0.63
+ mapperMatchScore: 128.0
+ mapperMismatchPenalty: -0.1
+ mapperOffsetShiftPenalty: -0.3
+ mapperMinSeedsDistance: 8
+ mapperMaxSeedsDistance: 18
+ minAlignmentLength: 15
+ maxAdjacentIndels: 2
+ alignmentStopPenalty: -1000
+ absoluteMinScore: 40.0
+ relativeMinScore: 0.87
+ maxHits: 4
+ scoring:
+ type: linear
+ alphabet: nucleotide
+ subsMatrix: "simple(match = 5, mismatch = -9)"
+ gapPenalty: -12
+ vjAlignmentOrder: VThenJ
+ libraryStructure: Unknown
+ includeDScore: false
+ includeCScore: false
+ minSumScore: 120.0
+ relativeMinVFR3CDR3Score: 0.7
+ allowPartialAlignments: true
+ allowNoCDR3PartAlignments: true
+ allowChimeras: false
+ readsLayout: Opposite
+ mergerParameters:
+ qualityMergingAlgorithm: MaxSubtraction
+ partsLayout: null
+ minimalOverlap: 13
+ minimalMatchQualitySum: 364
+ maxQuality: 50
+ minimalIdentity: 0.7
+ identityType: MinimalQualityWeighted
+ fixSeed: true
+ alignmentBoundaryTolerance: 5
+ minChimeraDetectionScore: 120
+ vjOverlapWindow: 3
+ saveOriginalSequence: false
+ saveOriginalReads: false
+ smartForceEdgeAlignments: true
+refineTagsAndSort:
+ whitelists: {}
+ runCorrection: true
+ parameters:
+ correctionPower: 0.001
+ backgroundSubstitutionRate: 0.001
+ backgroundIndelRate: 1.0E-5
+ minQuality: 12
+ maxSubstitutions: 2
+ maxIndels: 2
+ maxTotalErrors: 3
+ postFilter:
+ type: filter_groups
+ groupingKeys:
+ - allTags:Molecule
+ predicates:
+ - metrics:
+ - type: group_metric_sum_weight
+ reportHist:
+ log: true
+ binNumber: 0
+ minBinWidth: 0.2
+ multiplyWeightByKey: false
+ operator:
+ type: group_operator_lowest_threshold
+ operators:
+ - type: group_operator_advanced_thresholding
+ algo:
+ type: otsu
+ histTransformers:
+ - type: inflate
+ fraction: 0.15
+ value: 1.0
+ logX: true
+ minimalSample: 20
+ fallbackThreshold: 1.0
+ accept: High
+ - type: group_operator_cumtop
+ share: 0.85
+ round: Down
+ accept: High
+ accept: High
+ expectedSorting: []
+ requiredSequences: []
+ expectedSorting:
+ - allTags:Molecule
+ requiredSequences: []
+assemblePartial:
+ overlappedOnly: false
+ dropPartial: false
+ cellLevel: false
+ parameters:
+ kValue: 12
+ kOffset: -7
+ minimalAssembleOverlap: 12
+ minimalNOverlap: 7
+ minimalNOverlapShare: 0.65
+ minimalAlignmentMergeIdentity: 0.85
+ mergerParameters:
+ qualityMergingAlgorithm: SumSubtraction
+ partsLayout: CollinearDirect
+ minimalOverlap: 20
+ minimalMatchQualitySum: 0
+ maxQuality: 45
+ minimalIdentity: 0.95
+ identityType: Unweighted
+ maxLeftParts: 256000
+ maxLeftMatches: 6144
+extend:
+ vAnchor: CDR3Begin
+ jAnchor: FR4Begin
+ minimalVScore: 50
+ minimalJScore: 50
+assemble:
+ sortBySequence: false
+ clnaOutput: false
+ cellLevel: false
+ consensusAssemblerParameters:
+ assembler:
+ aAssemblerParameters:
+ bandWidth: 4
+ scoring:
+ type: linear
+ alphabet: nucleotide
+ subsMatrix: "simple(match = 5, mismatch = -4)"
+ gapPenalty: -14
+ minAlignmentScore: 40
+ maxNormalizedAlignmentPenalty: 0.2
+ trimMinimalSumQuality: 0
+ trimReferenceRegion: false
+ maxQuality: 45
+ maxIterations: 6
+ minAltSeedQualityScore: 11
+ minAltSeedNormalizedPenalty: 0.35
+ altSeedPenaltyTolerance: 0.5
+ minRecordSharePerConsensus: 0.2
+ minRecordsPerConsensus: 0
+ minRecursiveRecordShare: 0.4
+ minQualityScore: 0
+ maxConsensuses: 3
+ minTagSuffixShare: 0.0
+ isolateChains: false
+ cloneAssemblerParameters:
+ assemblingFeatures:
+ - CDR3
+ minimalClonalSequenceLength: 12
+ qualityAggregationType: BetaScore
+ cloneClusteringParameters:
+ searchDepth: 2
+ allowedMutationsInNRegions: 1
+ searchParameters: twoMismatchesOrIndels
+ clusteringFilter:
+ type: advanced
+ correctionPower: 0.001
+ backgroundSubstitutionRate: 5.0E-4
+ backgroundIndelRate: 2.0E-4
+ cloneFactoryParameters:
+ vParameters:
+ maxAlignmentWidthLinear: 5
+ maxAlignmentWidthAffine: 500
+ jParameters:
+ maxAlignmentWidthLinear: 5
+ maxAlignmentWidthAffine: 500
+ cParameters:
+ maxAlignmentWidthLinear: 5
+ maxAlignmentWidthAffine: 500
+ dParameters:
+ relativeMinScore: null
+ absoluteMinScore: null
+ maxHits: null
+ scoring: null
+ separateByV: false
+ separateByJ: false
+ separateByC: false
+ maximalPreClusteringRatio: 1.0
+ preClusteringScoreFilteringRatio: 2.0
+ preClusteringCountFilteringRatio: 2.0
+ addReadsCountOnClustering: false
+ badQualityThreshold: 15
+ maxBadPointsPercent: 0.7
+ mappingThreshold: 2of5
+ minimalQuality: 20
+ postFilters: null
+ inferMinRecordsPerConsensus: true
+assembleContigs:
+ ignoreTags: false
+ parameters:
+ branchingMinimalQualityShare: 0.1
+ branchingMinimalSumQuality: 60
+ decisiveBranchingSumQualityThreshold: 120
+ alignedSequenceEdgeDelta: 3
+ alignmentEdgeRegionSize: 7
+ minimalNonEdgePointsFraction: 0.25
+ minimalMeanNormalizedQuality: 5.0
+ outputMinimalQualityShare: 0.75
+ outputMinimalSumQuality: 0
+ subCloningRegions: null
+ assemblingRegions: null
+ postFiltering:
+ type: NoFiltering
+ trimmingParameters:
+ averageQualityThreshold: 10.0
+ windowSize: 8
+ minimalContigLength: 20
+ alignedRegionsOnly: false
+ discardAmbiguousNucleotideCalls: false
+exportAlignments:
+ chains: ALL
+ noHeader: false
+ fields:
+ - field: -readIds
+ - field: -tags
+ args:
+ - Molecule
+ - field: -targetSequences
+ - field: -targetQualities
+ - field: -vHitsWithScore
+ - field: -dHitsWithScore
+ - field: -jHitsWithScore
+ - field: -cHitsWithScore
+ - field: -vAlignments
+ - field: -dAlignments
+ - field: -jAlignments
+ - field: -cAlignments
+ - field: -allNFeaturesWithMinQuality
+ - field: -allAAFeatures
+ - field: -defaultAnchorPoints
+ - field: -topChains
+exportClones:
+ splitByTagType: null
+ filterOutOfFrames: false
+ filterStops: false
+ chains: ALL
+ noHeader: false
+ fields:
+ - field: -cloneId
+ - field: -readCount
+ - field: -readFraction
+ - field: -uniqueTagCount
+ args:
+ - Molecule
+ - field: -uniqueTagFraction
+ args:
+ - Molecule
+ - field: -targetSequences
+ - field: -targetQualities
+ - field: -vHitsWithScore
+ - field: -dHitsWithScore
+ - field: -jHitsWithScore
+ - field: -cHitsWithScore
+ - field: -vAlignments
+ - field: -dAlignments
+ - field: -jAlignments
+ - field: -cAlignments
+ - field: -allNFeaturesWithMinQuality
+ - field: -allAAFeatures
+ - field: -defaultAnchorPoints
+ splitFilesBy:
+ - chain
+ groupClonesBy: []