@transform([filterSNPs, filterIndels], regex(r'.*?([^/]+)\.vcf'), 
    [r'%s/\1.ensembl.vcf' % ensembl_dir,ensembl_dir % r'%s/\1.getEnsemblAnnotations.Success'])
def getEnsemblAnnotations(inputs, outputs):
    """
    Annotate vcf using ENSEMBL variant effect predictor.
    """
    vcf, _idx, _success = inputs
    output, flag_file = outputs
    logFile = mkLogFile(logDir, vcf, '.EnsemblAnnotation.log')
    print "Annotating %s with ENSEMBL variant effect predictor" % os.path.basename(vcf)
    runStageCheck('annotateEnsembl', flag_file, vcf, output, logFile)


# Indexing steps
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/getEnsemblAnnotations/swapped operands of `%`