def getOptionDefaults(self) : self.configScriptDir=scriptDir defaults=StrelkaSharedWorkflowOptionsBase.getOptionDefaults(self) libexecDir=defaults["libexecDir"] configDir=os.path.abspath(os.path.join(scriptDir,"@THIS_RELATIVE_CONFIGDIR@")) assert os.path.isdir(configDir) defaults.update({ 'runDir' : 'StrelkaGermlineWorkflow', 'strelkaGermlineBin' : joinFile(libexecDir,exeFile("starling2")), 'bgzip9Bin' : joinFile(libexecDir, exeFile("bgzip9")), 'configDir' : configDir, 'germlineSnvScoringModelFile' : joinFile(configDir,'germlineSNVScoringModels.json'), 'germlineIndelScoringModelFile' : joinFile(configDir,'germlineIndelScoringModels.json'), 'rnaSnvScoringModelFile' : joinFile(configDir,'RNASNVScoringModels.json'), 'rnaIndelScoringModelFile' : joinFile(configDir,'RNAIndelScoringModels.json'), 'callContinuousVf' : [], 'getCountsBin' : joinFile(libexecDir,exeFile("GetSequenceErrorCounts")), 'mergeCountsBin' : joinFile(libexecDir,exeFile("MergeSequenceErrorCounts")), 'estimateVariantErrorRatesBin' : joinFile(libexecDir,exeFile("EstimateVariantErrorRates")), 'thetaParamFile' : joinFile(configDir,'theta.json'), 'indelErrorRateDefault' : joinFile(configDir,'indelErrorModel.json'), 'isEstimateSequenceError' : True, 'isErrorEstimationFromAllData' : False }) return defaults
def getOptionDefaults(self): self.configScriptDir = scriptDir defaults = StrelkaSharedWorkflowOptionsBase.getOptionDefaults(self) libexecDir = defaults["libexecDir"] configDir = os.path.abspath( os.path.join(scriptDir, "@THIS_RELATIVE_CONFIGDIR@")) assert os.path.isdir(configDir) defaults.update({ 'runDir': 'StrelkaSomaticWorkflow', 'strelkaSomaticBin': joinFile(libexecDir, exeFile("strelka2")), 'minTier2Mapq': 0, 'snvScoringModelFile': joinFile(configDir, 'somaticSNVScoringModels.json'), 'indelScoringModelFile': joinFile(configDir, 'somaticIndelScoringModels.json'), 'isOutputCallableRegions': False, 'noiseVcfList': None }) return defaults
def getOptionDefaults(self) : self.configScriptDir=scriptDir defaults=StrelkaSharedWorkflowOptionsBase.getOptionDefaults(self) libexecDir=defaults["libexecDir"] configDir=os.path.abspath(os.path.join(scriptDir,"@THIS_RELATIVE_CONFIGDIR@")) assert os.path.isdir(configDir) defaults.update({ 'runDir' : 'SequenceAlleleCountsWorkflow', 'workflowScriptName' : 'runWorkflow.py', 'getCountsBin' : joinFile(libexecDir,exeFile("GetSequenceAlleleCounts")), 'mergeCountsBin' : joinFile(libexecDir,exeFile("MergeSequenceAlleleCounts")), 'extraCountsArguments' : None }) return defaults
def getOptionDefaults(self): """ Set option defaults. Every local variable in this method becomes part of the default hash """ configCommandLine = sys.argv libexecDir = os.path.abspath( os.path.join(scriptDir, "@THIS_RELATIVE_LIBEXECDIR@")) assert os.path.isdir(libexecDir) bgzipBin = joinFile(libexecDir, exeFile("bgzip")) htsfileBin = joinFile(libexecDir, exeFile("htsfile")) samtoolsBin = joinFile(libexecDir, exeFile("samtools")) tabixBin = joinFile(libexecDir, exeFile("tabix")) bgcatBin = joinFile(libexecDir, exeFile("bgzf_cat")) countFastaBin = joinFile(libexecDir, exeFile("countFastaBases")) getChromDepthBin = joinFile(libexecDir, exeFile("GetChromDepth")) mergeChromDepth = joinFile(libexecDir, "mergeChromDepth.py") catScript = joinFile(libexecDir, "cat.py") vcfCmdlineSwapper = joinFile(libexecDir, "vcfCmdlineSwapper.py") statsMergeBin = joinFile(libexecDir, exeFile("MergeRunStats")) workflowScriptName = "runWorkflow.py" # default memory request per process-type # # where different values are provided for SGE and local runs note: # 1. for SGE the memory limits must be greater than the highest memory use ever # expected in a production run. The consequence of exceeding this limit is a failed # run. # 2. for localhost the memory usage should be at least above the highest mean memory # use ever expected in a production run. The consequence of exceeding the mean is # a slow run due to swapping. # callSGEMemMb = 4 * 1024 callLocalMemMb = 2 * 1024 runDir = "variantCallWorkflow" # extended options scanSizeMb = 12 regionStrList = None callMemMbOverride = None isExome = False # isRNA is shared by all Strelka workflows, but only can be set for the germline calling case: isRNA = False isRetainTempFiles = False # Empirical Variant Scoring: isEVS = True isReportEVSFeatures = False indelErrorModelName = None inputIndelErrorModelsFile = None snvScoringModelFile = None indelScoringModelFile = None # error estimation is planned for all workflows, but can only be set true in germline at present: isEstimateSequenceError = False errorEstimationMinChromMb = 5 errorEstimationMinTotalMb = 50 return cleanLocals(locals())
def getOptionDefaults(self): """ Set option defaults. Every local variable in this method becomes part of the default hash """ configCommandLine = sys.argv alignerMode = "isaac" libexecDir = os.path.abspath( os.path.join(scriptDir, "@THIS_RELATIVE_LIBEXECDIR@")) assert os.path.isdir(libexecDir) bgzipBin = joinFile(libexecDir, exeFile("bgzip")) htsfileBin = joinFile(libexecDir, exeFile("htsfile")) tabixBin = joinFile(libexecDir, exeFile("tabix")) samtoolsBin = joinFile(libexecDir, exeFile("samtools")) mantaStatsBin = joinFile(libexecDir, exeFile("GetAlignmentStats")) mantaMergeStatsBin = joinFile(libexecDir, exeFile("MergeAlignmentStats")) getChromDepthBin = joinFile(libexecDir, exeFile("GetChromDepth")) mantaGraphBin = joinFile(libexecDir, exeFile("EstimateSVLoci")) mantaGraphMergeBin = joinFile(libexecDir, exeFile("MergeSVLoci")) mantaStatsMergeBin = joinFile(libexecDir, exeFile("MergeEdgeStats")) mantaGraphCheckBin = joinFile(libexecDir, exeFile("CheckSVLoci")) mantaHyGenBin = joinFile(libexecDir, exeFile("GenerateSVCandidates")) mantaGraphStatsBin = joinFile(libexecDir, exeFile("SummarizeSVLoci")) mantaStatsSummaryBin = joinFile(libexecDir, exeFile("SummarizeAlignmentStats")) mergeChromDepth = joinFile(libexecDir, "mergeChromDepth.py") mantaSortVcf = joinFile(libexecDir, "sortVcf.py") mantaExtraSmallVcf = joinFile(libexecDir, "extractSmallIndelCandidates.py") mantaPloidyFilter = joinFile(libexecDir, "ploidyFilter.py") mantaSortEdgeLogs = joinFile(libexecDir, "sortEdgeLogs.py") catScript = joinFile(libexecDir, "cat.py") vcfCmdlineSwapper = joinFile(libexecDir, "vcfCmdlineSwapper.py") mantaSortBam = joinFile(libexecDir, "sortBam.py") mantaMergeBam = joinFile(libexecDir, "mergeBam.py") mantaFilterBam = joinFile(libexecDir, "filterBam.py") # default memory request per process-type # # where different values are provided for SGE and local runs note: # 1. for SGE the memory limits must be greater than the highest memory use ever # expected in a production run. The consequence of exceeding this limit is a failed # run. # 2. for localhost the memory usage should be at least above the highest mean memory # use ever expected in a production run. The consequence of exceeding the mean is # a slow run due to swapping. # estimateMemMb = 2 * 1024 mergeMemMb = 4 * 1024 hyGenSGEMemMb = 4 * 1024 hyGenLocalMemMb = 2 * 1024 scanSizeMb = 12 return cleanLocals(locals())
def getOptionDefaults(self) : """ Set option defaults. Every local variable in this method becomes part of the default hash """ alignerMode = "isaac" libexecDir=os.path.abspath(os.path.join(scriptDir,"@THIS_RELATIVE_LIBEXECDIR@")) assert os.path.isdir(libexecDir) bgzipBin=joinFile(libexecDir,exeFile("bgzip")) htsfileBin=joinFile(libexecDir,exeFile("htsfile")) tabixBin=joinFile(libexecDir,exeFile("tabix")) mantaStatsBin=joinFile(libexecDir,exeFile("GetAlignmentStats")) mantaMergeStatsBin=joinFile(libexecDir,exeFile("MergeAlignmentStats")) mantaGetChromDepthBin=joinFile(libexecDir,exeFile("GetChromDepth")) mantaGraphBin=joinFile(libexecDir,exeFile("EstimateSVLoci")) mantaGraphMergeBin=joinFile(libexecDir,exeFile("MergeSVLoci")) mantaStatsMergeBin=joinFile(libexecDir,exeFile("MergeEdgeStats")) mantaGraphCheckBin=joinFile(libexecDir,exeFile("CheckSVLoci")) mantaHyGenBin=joinFile(libexecDir,exeFile("GenerateSVCandidates")) mantaGraphStatsBin=joinFile(libexecDir,exeFile("SummarizeSVLoci")) mantaStatsSummaryBin=joinFile(libexecDir,exeFile("SummarizeAlignmentStats")) mergeChromDepth=joinFile(libexecDir,"mergeChromDepth.py") mantaSortVcf=joinFile(libexecDir,"sortVcf.py") mantaExtraSmallVcf=joinFile(libexecDir,"extractSmallIndelCandidates.py") mantaPloidyFilter=joinFile(libexecDir,"ploidyFilter.py") mantaSortEdgeLogs=joinFile(libexecDir,"sortEdgeLogs.py") mantaCat=joinFile(libexecDir,"cat.py") # default memory request per process-type # # where different values are provided for SGE and local runs note: # 1. for SGE the memory limits must be greater than the highest memory use ever # expected in a production run. The consequence of exceeding this limit is a failed # run. # 2. for localhost the memory usage should be at least above the highest mean memory # use ever expected in a production run. The consequence of exceeding the mean is # a slow run due to swapping. # estimateMemMb=2*1024 mergeMemMb=4*1024 hyGenSGEMemMb=4*1024 hyGenLocalMemMb=2*1024 scanSizeMb = 12 return cleanLocals(locals())