@transform(dedup, suffix('.bam'),
            ['.bam.tdf', '.bam.igvcountDedupedBams.Success'])
def igvcountDedupedBams(inputs, outputs):
    """
    Use igvtools count to create a .tdf file for the deduped bam files, to improve viewing of the bam coverage in igv. Note that this actually goes from the fixMate-ed bams.
    """
    bam, _success = inputs
    outfile, flag_file = outputs
    print os.path.basename(bam) % "igvtools count on %s"
    runStageCheck('igvcount', flag_file, bam, outfile)
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/igvcountDedupedBams/swapped operands of `%`