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defaults.yml
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remoteDataURL: http://174.129.238.44/export/AAVengeR/data
system_minMemThreshold: 80
system_minMemWaitTime: 1200
system_minMemSleepTime: 10
core_createFauxFragDoneFiles: FALSE
core_createFauxSiteDoneFiles: FALSE
buildStdFragments_minRemnantLengthToGroup: 12
core_processMaxPercentCPU: 15
core_processMaxCPUs: 10
calledFromCore: FALSE
core_CPUs: 15
databaseConfigFile: /home/ubuntu/.my.cnf
databaseConfigGroup: none
sequencingRunID: xxx
Rscript: /usr/bin/Rscript
compressDataFiles: FALSE
processAdriftReadLinkerUMIs: FALSE
core_keepIntermediateFiles: FALSE
core_applyCoreCPUsToAllModules: TRUE
demultiplex_CPUs: 15
demultiplex_outputDir: demultiplex
demultiplex_replicateMergingInstructions: none
demultiplex_level: unique
demultiplex_quickAlignFilter: FALSE
demultiplex_useAdriftReadUniqueLinkers: TRUE
demultiplex_requirePostUmiLinker: TRUE
demultiplex_requirePostUmiLinker_maxMismatch: 2
demultiplex_RC_I1_barcodes: FALSE
demultiplex_RC_I1_barcodes_auto: TRUE
demultiplex_qualtrim_code: '+'
demultiplex_qualtrim_halfWidth: 3
demultiplex_qualtrim_events: 2
demultiplex_qualtrim_minLength: 50
demultiplex_correctGolayIndexReads: FALSE
demultiplex_sequenceChunkSize: 300000
demultiplex_index1ReadMaxMismatch: 1
demultiplex_adriftReadLinkerBarcodeMaxMismatch: 1
demultiplex_anchorReadStartSeq.maxMisMatch: 1
demultiplex_exportFASTQ: FALSE
demultiplex_quickAlignFilter_minPercentID: 97
demultiplex_quickAlignFilter_minMatches: 30
demultiplex_quickAlignFilter_minEstLeaderSeqLength: 15
demultiplex_mergeSimilarReadPairsParams: -c 0.98 -d 0 -M 0 -g 1 -r 0 -ap 1 -G 0 -n 5 -gap -10 -gap-ext -5 -aS 0.98 -aL 0.98
prepReads_CPUs: 15
prepReads_outputDir: prepReads
prepReads_excludeAnchorReadVectorHits: TRUE
prepReads_excludeAdriftReadVectorHits: FALSE
prepReads_vectorAlignmentTestLength: 25
prepReads_vectorAlignmentTest_minPercentCoverage: 90
prepReads_vectorAlignmentTest_minPercentID: 90
prepReads_minAnchorReadLength: 20
prepReads_minAdriftReadLength: 20
prepReads_buildReadMaps_blastReconstruction: TRUE
prepReads_mapLeaderSeqsMinAlignmentLength: 15
prepReads_mapLeaderSeqsMinPercentID: 95
prepReads_mapLeaderSeqsMaxGapBetweenAlignments: 5
prepReads_buildReadMaps_minMapStartPostion: 5
prepReads_useDefaultHMMsettings: TRUE
prepReads_HMMsearchReadStartPos: 1
prepReads_HMMsearchReadEndPos: 100
prepReads_HMMmaxStartPos: 5
prepReads_HMMminFullBitScore: 20
prepReads_HMMmatchEnd: TRUE
prepReads_HMMmatchTerminalSeq: CA
prepReads_forceAnchorReadStartSeq: FALSE
prepReads_limitLeaderSeqsWithQuickAlignFilter: TRUE
prepReads_additionalAnchorReadOverReadingSeqs: none
prepReads_cutAdaptErrorRate: 0.15
alignReads_CPUs: 15
alignReads_outputDir: alignReads
alignReads_blat_fastMap: FALSE
alignReads_blatUseOocFile: FALSE
alignReads_genomeAlignment_anchorRead_maxStartPos: 3
alignReads_genomeAlignment_adriftRead_maxStartPos: 3
alignReads_genomeAlignment_minPercentID: 95
alignReads_genomeAlignment_blatStepSize: 5
alignReads_genomeAlignment_blatTileSize: 11
alignReads_genomeAlignment_blatRepMatch: 3000
alignReads_genomeAlignment_blatMaxtNumInsert: 1
alignReads_genomeAlignment_blatMaxqNumInsert: 1
alignReads_genomeAlignment_blatMaxtBaseInsert: 1
alignReads_genomeAlignment_blatMaxqBaseInsert: 1
alignReads_genomeAlignment_anchorReadEnd_maxUnaligned: 5
alignReads_genomeAlignment_adriftReadEnd_maxUnaligned: 5
buildFragments_CPUs: 15
buildFragments_outputDir: buildFragments
buildFragments_anchorReadsAlignmentFile: alignReads/anchorReadAlignments.rds
buildFragments_adriftReadsAlignmentFile: alignReads/adriftReadAlignments.rds
buildFragments_idGroup_size: 500
buildFragments_maxReadAlignments: 1500
buildFragments_salvageReadsBeyondMaxNumAlignments: TRUE
buildFragments_minFragLength: 50
buildFragments_maxFragLength: 3000
buildFragments_randomLinkerID_minReadCountToSegreagate: 10
buildFragments_randomLinkerID_minSingleSampleMajorityPercent: 90
buildStdFragments_CPUs: 15
buildStdFragments_outputDir: buildStdFragments
buildStdFragments_randomIDdupReadMult: 3
buildStdFragments_randomIDdupAbundMult: 2
buildStdFragments_clusterLeaderSeqs: TRUE
buildStdFragments_standardizeIntegrationPositions: TRUE
buildStdFragments_standardizeBreakPositions: TRUE
buildStdFragments_standardizeBreakPositionsWithin: replicates
buildStdFragments_intSiteStdWindowWidth: 5
buildStdFragments_breakPointStdWindowWidth: 3
buildStdFragments_minReadsPerFrag: 1
buildStdFragments_createMultiHitClusters: TRUE
buildStdFragments_salvageMultiHitReads: FALSE
buildStdFragments_UMIminPercentReads: 15
buildStdFragments_remnantClusterParams: -c 0.85 -d 0 -M 0 -g 1 -r 0 -ap 1 -G 0 -n 5 -gap -5 -gap-ext -1 -aS 0.85 -aL 0.85
buildStdFragments_evalFragAnchorReadSeqs: TRUE
buildStdFragments_fragEvalAnchorReadTestLen: 30
buildStdFragments_fragClusterParams: -c 0.87 -d 0 -M 0 -g 1 -r 0 -ap 1 -G 0 -n 5 -gap -10 -gap-ext -5 -aS 0.95 -aL 0.95
buildStdFragments_fragEvalAnchorReadMinAbundDiff: 5
buildStdFragments_fragEvalAnchorReadMinReadMult: 10
buildSites_CPUs: 15
buildSites_outputDir: buildSites
buildSites_enableDualDetection: TRUE
buildSites_integraseCorrectionDist: 0
buildSites_dualDetectWidth: 6
buildSites_sumSonicBreaksWithin: samples
annotateRepeats_CPUs: 15
annotateRepeats_outputDir: annotateRepeats
annotateRepeats_addAfter: nRepsObs
callNearestGenes_CPUs: 15
callNearestGenes_inputFile: core/sites.rds
callNearestGenes_outputDir: callNearestGenes
callNearestGenes_addAfter: nRepsObs
callNearestGenes_columnPrefix: none
callNearestGenes_TU_position: either
callNearestGenes_boundaries:
hg38:
TUs: hg38.TUs.rds
exons: hg38.exons.rds
sacCer3:
TUs: sacCer3.TUs.rds
exons: sacCer3.exons.rds
canFam3:
TUs: canFam3.humanXenoRef.TUs.rds
exons: canFam3.humanXenoRef.exons.rds
macFas5:
TUs: macFas5.humanXenoRef.TUs.rds
exons: macFas5.humanXenoRef.exons.rds
mapSiteLeaderSequences_CPUs: 15
mapSiteLeaderSequences_outputDir: mapSiteLeaderSequences
mapSiteLeaderSequences_addAfter: repLeaderSeq
mapSiteLeaderSequences_minLocalAlignmentLength: 12
mapSiteLeaderSequences_minAlignmentPercentID: 90
mapSiteLeaderSequences_minAlignmentLength: 15
mapSiteLeaderSequences_maxMissingTailNTs: 5
predictPCRartifacts_CPUs: 15
predictPCRartifacts_outputDir: predictPCRartifacts
predictPCRartifacts_adjacentSeqLength: 14
predictPCRartifacts_minReportHalfMatches: 5
predictPCRartifacts_minReportMatches: 10
predictPCRartifacts_maxAlnGaps: 1
predictPCRartifacts_wordSize: 5
predictPCRartifacts_gapOpeningPenalty: 10
predictPCRartifacts_gapExtensionPenalty: 5
predictPCRartifacts_addAfter: posid
barcodeAssocLinkers_outputDir: barcodeAssocLinkers
barcodeAssocLinkers_nCodes: 50
barcodeAssocLinkers_excludePolyG_index1BarCodes: TRUE
barcodeAssocLinkers_adriftReadUniqueLinkerLength: 20
buildAAVremnantPlots_outputDir: buildAAVremnantPlots
buildAAVremnantPlots_NTbinSize: 3
buildAAVremnantPlots_ITRlength: 197
buildAAVremnantPlots_ITRseqStart: 57
buildAAVremnantPlots_ITRdumbellTip1: 125
buildAAVremnantPlots_ITRdumbellTip2: 147
buildAAVremnantPlots_plotOutputWidthInches: 10
callNearestGenesFiltered_CPUs: 15
callNearestGenesFiltered_columnPrefix: oncoGenes
callNearestGenesFiltered_outputDir: callNearestGenesFiltered
callNearestGenesFiltered_addAfter: nRepsObs
callNearestGenesFiltered_TU_position: either
callNearestGenesFiltered_boundaries:
hg38:
TUs: hg38.TUs.rds
exons: hg38.exons.rds
filter: hg38.Bushman.oncoGeneList.rds
sacCer3:
TUs: sacCer3.TUs.rds
exons: sacCer3.exons.rds
filter: hg38.Bushman.oncoGeneList.rds
canFam3:
TUs: canFam3.humanXeno.TUs.rds
exons: canFam3.humanXeno.exons.rds
filter: hg38.Bushman.oncoGeneList.rds
macFas5:
TUs: macFas5.humanXeno.TUs.rds
exons: macFas5.humanXeno.exons.rds
filter: hg38.Bushman.oncoGeneList.rds
anchorReadRearrangements_CPUs: 15
anchorReadRearrangements_outputDir: anchorReadRearrangements
anchorReadRearrangements_vectorLeaderSeqFilterLength: 12
anchorReadRearrangements_vectorLeaderSeqFilterMaxMismatch: 1
anchorReadRearrangements_qualtrim_events: 2
anchorReadRearrangements_qualtrim_code: '5'
anchorReadRearrangements_qualtrim_halfWidth: 5
anchorReadRearrangements_minReadOverlapNTs: 20
anchorReadRearrangements_maxReadOverlapPval: 0.001
anchorReadRearrangements_anchorReadCutPos: 200
anchorReadRearrangements_requireReadPairOverlap: TRUE
anchorReadRearrangements_minReadsPerAltStruct: 2
anchorReadRearrangements_cutAdaptErrorRate: 0.15
anchorReadRearrangements_minAlignmentLength: 10
anchorReadRearrangements_minAlignmentPercentID: 90
anchorReadRearrangements_maxMissingTailNTs: 11
anchorReadRearrangements_readEndAlignmentTestLength: 12
anchorReadRearrangements_readEndAlignmentTestMinMatch: 11
anchorReadRearrangements_clusterParams: -c 0.90 -d 0 -aS 0.93 -M 0 -g 1 -r 0 -ap 1 -G 0 -n 5 -gap -5 -gap-ext -1