process NORMALISE {
    tag "$vcf.simpleName"
    input:  path vcf
    output: path "${vcf.simpleName}.norm.vcf.gz", emit: vcf

    // Split multiallelics, then set each ID to CHROM_POS_REF_ALT. VEP echoes the ID back as
    // Uploaded_variation, and the loader takes exact VCF alleles from it (VEP trims indels).
    script:
    """
    bcftools norm -m -both -Ou $vcf \\
        | bcftools annotate --set-id '%CHROM\\_%POS\\_%REF\\_%FIRST_ALT' -Oz -o ${vcf.simpleName}.norm.vcf.gz
    """

    stub:
    """
    touch ${vcf.simpleName}.norm.vcf.gz
    """
}