@transform(filterIndels, suffix('.vcf'),
            ['.vcf.gz', '.vcf.gz.tbi', '.vcfindexIndels.Success'])
def vcfIndexIndels(inputs, outputs):
    """
    Use bgzip and tabix to prepare raw indels vcf for vcftools handling.
    """
    vcf, _idx, _success = inputs
    zipfile, tabix_index, flag_file = outputs
    print vcf % "bgzip and tabix (for vcftools) on %s"
    runStageCheck('indexVCF', flag_file, vcf)


# Coverage steps
dataset/ETHPy150Open vlsci/variant_calling_pipeline/pipeline.py/vcfIndexIndels/swapped operands of `%`