@transform(callIndels, suffix('.INDEL.vcf'),
            ['.INDEL.filtered.vcf', '.INDEL.filtered.vcf.idx', '.filterIndels.Success'])
def filterIndels(inputs, outputs):
    """
    Use GATK VariantFiltration to filter raw INDEL calls.
    """
    input_vcf, _idx, _success = inputs
    output_vcf, _idxout, flag_file = outputs
    logFile = mkLogFile(logDir, input_vcf, '.filterIndels.log')
    print input_vcf % "filtering indels from %s"
    runStageCheck('filterIndels', flag_file, ref_files['fasta_reference'], input_vcf, logFile, output_vcf)
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/filterIndels/swapped operands of `%`