@transform(bwaPE, suffix(".sam"),
            [".bam", ".samToBam.Success"])
def samToBam(inputs, outputs):
    """
    Convert sam to bam and sort, using Picard.
    """
    output, flag_file = outputs
    sam, _success = inputs
    print os.path.basename(sam) % "converting to sorted bam: %s"
    runStageCheck('samToSortedBam', flag_file, sam, output)
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/samToBam/swapped operands of `%`