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)