@follows('indexRealignedBams')
@transform(realign, suffix('.bam'),
            ['.recal_data.csv', '.baseQualRecalCount.Success'])
def baseQualRecalCount(inputs, outputs):
    """
    GATK CountCovariates, first step of base quality score recalibration.
    """
    bam, _success = inputs
    output_csv, flag_file = outputs
    logFile = mkLogFile(logDir, bam, '.baseQualRecalCount.log')
    print os.path.basename(bam) % "count covariates using GATK for base quality score recalibration: %s"
    runStageCheck('baseQualRecalCount', flag_file, bam, ref_files['fasta_reference'], ref_files['dbsnp'], logFile, output_csv)
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/baseQualRecalCount/swapped operands of `%`