@transform(baseQualRecalTabulate, suffix('.bam'),
            ['.bam.bai', '.bam.indexRecalibratedBams.Success'])
def indexRecalibratedBams(inputs, outputs):
    """
    Index the recalibrated bams using samtools. 
    """
    bam, _success = inputs
    output, flag_file = outputs
    print os.path.basename(bam) % "samtools index on %s"
    runStageCheck('indexBam', flag_file, bam)

# Variant calling steps
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/indexRecalibratedBams/swapped operands of `%`