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"]
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 __init__(self, params, iniSections):
global PathInfo
super(StrelkaGermlineWorkflow, self).__init__(params, iniSections,
PathInfo)
# format bam lists:
if self.params.bamList is None: self.params.bamList = []
# format other:
safeSetBool(self.params, "isWriteRealignedBam")
if self.params.isWriteRealignedBam:
self.params.realignedDir = os.path.join(self.params.resultsDir,
"realigned")
ensureDir(self.params.realignedDir)
if self.params.isExome:
self.params.isEVS = False
if self.params.isRNA:
self.params.germlineSnvScoringModelFile = joinFile(
self.params.configDir, 'RNAVariantScoringModels.json')
self.params.germlineIndelScoringModelFile = None
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
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) :
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) :
"""
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())
