@follows(indexRecalibratedBams)
@transform(baseQualRecalTabulate, 
            regex(r'(.*?)([^/]+)\.recal\.bam'),
            [r'%s/\2.INDEL.vcf' % variant_dir, 
             variant_dir % r'%s/\2.INDEL.vcf.idx', 
             r'%s/\2.callIndels.Success' % variant_dir])
def callIndels(inputs, outputs):
    """
    Use GATK UnifiedGenotyper to call indels from recalibrated bams.
    """
    bam, _success = inputs
    output_vcf, _idx, flag_file = outputs
    logFile = mkLogFile(logDir, bam, '.callIndels.log')
    print "calling Indels from %s" % bam
    runStageCheck('callIndels', flag_file, ref_files['fasta_reference'], bam, ref_files['dbsnp'], logFile, output_vcf)
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/callIndels/swapped operands of `%`