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

flowcellFastqDir
    flowcellBamDir

    calls:
    FastqPairToBwaBamFlow
        supplies:
        bamFile
        fastq1File
        fastq2File
    """

    #
    # 1. separate fastqs into matching pairs:
    #
    fqs = {}
    fqDigger = FileDigger(".fastq.gz", ["Project_", "Sample_"])
    for (project, sample, fqPath) in fqDigger.getNextFile(self.params.flowcellFastqDir) :
        if (self.params.sampleNameList != None) and \
           (len(self.params.sampleNameList) != 0) and \
           (sample not in self.params.sampleNameList) : continue

        fqFile = os.path.basename(fqPath)
        w = (fqFile.split(".")[0]).split("_")
        if len(w) != 5 :
            raise Exception("Unexpected fastq filename format: '%s'" % (fqPath))

        (sample2, index, lane, read, num) = w
        if sample != sample2 :
            raise Exception("Fastq name sample disagrees with directory sample: '%s;" % (fqPath))

        key = (project, sample, index, lane, num)
        if key not in fqs : fqs[key] = [None, None]

self.params.mergeBamList = bams[key]
            self.params.mergeBamName = os.path.join(mergedSampleDir, sample + mergedBamExt)
            mergedBams[key] = self.params.mergeBamName
            outTaskPrefix = preJoin(taskPrefix, "_".join(key))
            sampleTasks[key] = mergeBamListFlow(self, outTaskPrefix, dependencies)

    if not os.path.isdir(mergedBamDir) : return


    #
    # 3) mark dup:
    #

    # mergedBams contains all bams from the current run, we also add any from a
    # previous interupted run:
    mergedBamDigger = FileDigger(mergedBamExt, ["Project_", "Sample_"])
    for (project, sample, bamFile) in mergedBamDigger.getNextFile(mergedBamDir) :
        key = (project, sample)
        if key in mergedBams :
            assert (mergedBams[key] == bamFile)
        else :
            mergedBams[key] = bamFile

    nextWait = set()
    totalCores = self.getNCores()

    for sampleKey in mergedBams.keys() :
        markDupDep = set()
        if sampleKey in sampleTasks : markDupDep = sampleTasks[sampleKey]

        fullName = "_".join(sampleKey)

supplies:
        mergeBamList
        mergeBamName
    """

    #
    # 1) get a list of bams associated with each project/sample combination:
    #

    # TODO: what if there's an NFS delay updating all the bams while
    # we're reading them out here? make this process more robust -- we
    # should know how many BAM's we're expecting, in a way that's
    # robust to interuption/restart
    #
    bams = {}
    bamDigger = FileDigger(".bam", ["Flowcell_", "bam", "Project_", "Sample_"])
    for (flowcell, nothing, project, sample, bamFile) in bamDigger.getNextFile(self.params.allFlowcellDir) :
        if (self.params.sampleNameList != None) and \
           (len(self.params.sampleNameList) != 0) and \
           (sample not in self.params.sampleNameList) : continue
        key = (project, sample)
        if key not in bams : bams[key] = []
        bams[key].append(bamFile)

    mergedBamExt = ".merged.bam"
    markDupBamExt = ".markdup.bam"

    #
    # 2) merge and delete smaller bams:
    #
    mergedBams = {}