def workflow(self):
self.flowLog("Initiating Strelka germline workflow version: %s" %
(__version__))
self.setCallMemMb()
callPreReqs = set()
estimatePreReqs = set()
estimatePreReqs.add(runCount(self))
if self.params.isHighDepthFilter:
estimatePreReqs |= strelkaGermlineGetDepthFromAlignments(self)
if self.params.isEstimateSequenceError:
validatePreReq = self.addWorkflowTask(
"EstimateSeqErrorParams",
EstimateSequenceErrorWorkflow(self.params, self.paths),
dependencies=estimatePreReqs)
callPreReqs.add(
self.addWorkflowTask("ValidateSeqErrorParams",
ValidateEstimatedParametersWorkflow(
self.params, self.paths),
dependencies=validatePreReq))
else:
callPreReqs = estimatePreReqs
self.addWorkflowTask("CallGenome",
CallWorkflow(self.params, self.paths),
dependencies=callPreReqs)
def workflow(self) :
self.flowLog("Initiating Strelka noise estimation workflow version: %s" % (__version__))
callPreReqs = set()
callPreReqs.add(runCount(self))
self.addWorkflowTask("CallGenome", CallWorkflow(self.params, self.paths), dependencies=callPreReqs)
def workflow(self) :
self.flowLog("Initiating Strelka somatic workflow version: %s" % (__version__))
self.setCallMemMb()
callPreReqs = set()
callPreReqs |= runCount(self)
if self.params.isHighDepthFilter :
callPreReqs |= strelkaSomaticRunDepthFromAlignments(self)
self.addWorkflowTask("CallGenome", CallWorkflow(self.params, self.paths), dependencies=callPreReqs)
