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)
configDir = os.path.abspath(
os.path.join(scriptDir, "@THIS_RELATIVE_CONFIGDIR@"))
assert os.path.isdir(configDir)
defaults.update({
'runDir': 'PedicureWorkflow',
'isOutputCallableRegions': False
})
return defaults
def getOptionDefaults(self) :
self.configScriptDir=scriptDir
defaults=StrelkaSharedWorkflowOptionsBase.getOptionDefaults(self)
libexecDir=defaults["libexecDir"]
defaults.update({
'runDir' : 'StrelkaNoiseWorkflow',
'workflowScriptName' : 'runWorkflow.py',
'bgcatBin' : joinFile(libexecDir,"bgzf_cat"),
'bgzip9Bin' : joinFile(libexecDir,"bgzip9"),
'snoiseBin' : joinFile(libexecDir,"strelkaNoiseExtractor")
})
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):
self.configScriptDir = scriptDir
defaults = StrelkaSharedWorkflowOptionsBase.getOptionDefaults(self)
configDir = os.path.abspath(
os.path.join(scriptDir, "@THIS_RELATIVE_CONFIGDIR@"))
assert os.path.isdir(configDir)
defaults.update({
'runDir':
'StrelkaSomaticWorkflow',
"minTier2Mapq":
0,
'somaticSnvScoringModelFile':
joinFile(configDir, 'somaticVariantScoringModels.json'),
'somaticIndelScoringModelFile':
None, #joinFile(configDir,'somaticVariantScoringModels.json'),
'isOutputCallableRegions':
False,
'noiseVcfList':
None
})
return defaults