Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
flowcellLabel = getFlowcellLabel(self, i)
flowcellDir = os.path.join(self.params.allFlowcellDir, flowcellLabel)
ensureDir(flowcellDir)
self.params.flowcellFastqDir = os.path.join(flowcellDir, "fastq")
self.params.flowcellBamDir = os.path.join(flowcellDir, "bam")
if self.params.bclTilePatternList == None :
self.params.bclTilePattern = None
else :
self.params.bclTilePattern = self.params.bclTilePatternList[i]
fastqFinal = casava18BclToFastqFlow(self, taskPrefix=flowcellLabel)
label = preJoin(taskPrefix, "_".join((flowcellLabel, "FastqToBwaBam")))
nextWait.add(self.addWorkflowTask(label, FlowcellDirFastqToBwaBamFlow(self.params), dependencies=fastqFinal))
return nextWait