How to use the pyflow.demo.bclToBwaBam.bwaworkflow.FlowcellDirFastqToBwaBamFlow function in pyflow

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github Illumina / pyflow / pyflow / demo / bclToBwaBam / bwaworkflow.py View on Github external
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