def main() :
primarySectionName="StrelkaSomatic"
options,iniSections=StrelkaSomaticWorkflowOptions().getRunOptions(primarySectionName,
version=workflowVersion)
# we don't need to instantiate the workflow object during configuration,
# but this is done here to trigger additional parameter validation:
#
StrelkaSomaticWorkflow(options)
# generate runscript:
#
ensureDir(options.runDir)
workflowScriptPath = os.path.join(options.runDir, options.workflowScriptName)
makeRunScript(workflowScriptPath,os.path.join(workflowDir,"strelkaSomaticWorkflow.py"),"StrelkaSomaticWorkflow",primarySectionName,iniSections)
notefp=sys.stdout
notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
%s
""" % (workflowScriptPath))
def main():
primarySectionName = "counts"
options, iniSections = SequenceErrorCountsWorkflowOptions().getRunOptions(
primarySectionName, version=workflowVersion)
# we don't need to instantiate the workflow object during configuration,
# but this is done here to trigger additional parameter validation:
#
SequenceErrorCountsWorkflow(options)
# generate runscript:
#
ensureDir(options.runDir)
scriptFile = os.path.join(options.runDir, "runWorkflow.py")
makeRunScript(scriptFile,
os.path.join(workflowDir, "sequenceErrorCountsWorkflow.py"),
"SequenceErrorCountsWorkflow", primarySectionName,
iniSections)
notefp = sys.stdout
notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
%s
""" % (scriptFile))
def main() :
if (sys.version_info[0] != 2):
notefp=sys.stdout
notefp.write("""Failed to create workflow run script.\nPyflow only supports python2. Detected python %s on the system.\n""" % sys.version_info[0])
return
primarySectionName="snoise"
options,iniSections=snoiseWorkflowOptions().getRunOptions(primarySectionName, version=workflowVersion)
# we don't need to instantiate the workflow object during configuration,
# but this is done here to trigger additional parameter validation:
#
snoiseWorkflow(options)
# generate runscript:
#
ensureDir(options.runDir)
workflowScriptPath = os.path.join(options.runDir, options.workflowScriptName)
makeRunScript(workflowScriptPath,os.path.join(workflowDir,"snoiseWorkflow.py"),"snoiseWorkflow",primarySectionName,iniSections)
notefp=sys.stdout
notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
%s
""" % (workflowScriptPath))
def __init__(self,params,iniSections) :
# clear out some potentially destabilizing env variables:
clearList = [ "PYTHONPATH", "PYTHONHOME"]
for key in clearList :
if key in os.environ :
del os.environ[key]
self.params=params
self.iniSections=iniSections
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
self.params.normalBamList = []
for bam in (self.params.normalBam,) :
if bam is None : continue
self.params.normalBamList.append(bam)
self.params.tumorBamList = []
for bam in (self.params.tumorBam,) :
if bam is None : continue
self.params.tumorBamList.append(bam)
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# sanity check some parameter typing:
self.params.binSize = int(self.params.binSize)
self.params.nonlocalWorkBins = int(self.params.nonlocalWorkBins)
self.paths = PathInfo(self.params)
def __init__(self, params) :
global PathInfo
super(SequenceAlleleCountsWorkflow, self).__init__(params, PathInfo)
# if debugging output is going to be produced, add a results/debug dir
if self.params.isReportObservedIndels:
self.params.debugDir=os.path.join(self.params.resultsDir,"debug")
ensureDir(self.params.debugDir)
# format bam lists:
if self.params.bamList is None : self.params.bamList = []
def __init__(self,params,iniSections) :
# clear out some potentially destabilizing env variables:
clearList = [ "PYTHONPATH", "PYTHONHOME"]
for key in clearList :
if key in os.environ :
del os.environ[key]
self.params=params
self.iniSections=iniSections
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# sanity check some parameter typing:
MEGABASE = 1000000
self.params.scanSize = int(self.params.scanSizeMb) * MEGABASE
self.params.nonlocalWorkBins = int(self.params.nonlocalWorkBins)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self,params) :
global PathInfo
super(StrelkaGermlineWorkflow,self).__init__(params,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
def __init__(self, params, iniSections):
cleanPyEnv()
self.params = params
self.iniSections = iniSections
# format bam lists:
if self.params.normalBamList is None: self.params.normalBamList = []
if self.params.tumorBamList is None: self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(indexRefFasta, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self, params, iniSections):
global PathInfo
super(StrelkaPedigreeWorkflow, self).__init__(params, iniSections,
PathInfo)
# format bam lists:
if self.params.probandBamList is None: self.params.probandBamList = []
if self.params.parentBamList is None: self.params.parentBamList = []
if self.params.siblingBamList is None: self.params.siblingBamList = []
# bools coming from the ini file need to be cleaned up:
safeSetBool(self.params, "isWriteRealignedBam")
if self.params.isOutputCallableRegions:
self.params.regionsDir = os.path.join(self.params.resultsDir,
"regions")
ensureDir(self.params.regionsDir)
def __init__(self,params) :
global PathInfo
super(StrelkaSomaticWorkflow,self).__init__(params, PathInfo)
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# bools coming from the ini file need to be cleaned up:
safeSetBool(self.params,"isWriteRealignedBam")
if self.params.isOutputCallableRegions :
self.params.regionsDir=os.path.join(self.params.resultsDir,"regions")
ensureDir(self.params.regionsDir)
if self.params.isWriteRealignedBam :
self.params.realignedDir=os.path.join(self.params.resultsDir,"realigned")
ensureDir(self.params.realignedDir)
def __init__(self,params,iniSections) :
cleanPyEnv()
self.params=params
self.iniSections=iniSections
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self, params, PathInfoType):
cleanPyEnv()
self.params = params
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transferred to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
# timings and other stats go into statsDir
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.paths = PathInfoType(self.params)
referenceFastaIndex = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(referenceFastaIndex, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(referenceFastaIndex)
# determine subset of chroms where we can skip calling entirely
self.params.chromIsSkipped = getChromIsSkipped(self)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))
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 main() :
primarySectionName="manta"
options,iniSections=MantaWorkflowOptions().getRunOptions(primarySectionName, version=workflowVersion)
# we don't need to instantiate the workflow object during configuration,
# but this is done here to trigger additional parameter validation:
#
MantaWorkflow(options,iniSections)
# generate runscript:
#
ensureDir(options.runDir)
scriptFile=os.path.join(options.runDir,"runWorkflow.py")
makeRunScript(scriptFile,os.path.join(workflowDir,"mantaWorkflow.py"),"MantaWorkflow",primarySectionName,iniSections)
notefp=sys.stdout
notefp.write("""
Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:
%s
""" % (scriptFile))
def __init__(self,params) :
cleanPyEnv()
self.params=params
# normalize boolean option input:
safeSetBool(self.params,"enableRemoteReadRetrievalForInsertionsInGermlineCallingModes")
safeSetBool(self.params,"enableRemoteReadRetrievalForInsertionsInCancerCallingModes")
safeSetBool(self.params,"useOverlapPairEvidence")
# Use RNA option for minCandidate size
if self.params.isRNA:
self.params.minCandidateVariantSize = self.params.rnaMinCandidateVariantSize
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
self.params.evidenceDir=os.path.join(self.params.resultsDir,"evidence")
ensureDir(self.params.evidenceDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# determine subset of chroms where we can skip calling entirely
(self.params.callRegionList, self.params.chromIsSkipped) = getCallRegions(self.params)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
# always use overlapping pairs for RNA calling
if (self.params.isRNA) :
self.params.useOverlapPairEvidence = True
def __init__(self, params):
cleanPyEnv()
self.params = params
# normalize boolean option input:
safeSetBool(
self.params,
"enableRemoteReadRetrievalForInsertionsInGermlineCallingModes")
safeSetBool(
self.params,
"enableRemoteReadRetrievalForInsertionsInCancerCallingModes")
safeSetBool(self.params, "useOverlapPairEvidence")
# Use RNA option for minCandidate size
if self.params.isRNA:
self.params.minCandidateVariantSize = self.params.rnaMinCandidateVariantSize
# format bam lists:
if self.params.normalBamList is None: self.params.normalBamList = []
if self.params.tumorBamList is None: self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
self.params.evidenceDir = os.path.join(self.params.resultsDir,
"evidence")
ensureDir(self.params.evidenceDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(indexRefFasta, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# determine subset of chroms where we can skip calling entirely
(self.params.callRegionList,
self.params.chromIsSkipped) = getCallRegions(self.params)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
# always use overlapping pairs for RNA calling
if (self.params.isRNA):
self.params.useOverlapPairEvidence = True
