process VEP {
    tag "$vcf.simpleName"
    publishDir params.outdir, mode: 'copy'
    input:  path vcf
    output:
        path "${vcf.simpleName}.vep.tsv",      emit: tsv
        path "${vcf.simpleName}.vep_summary.html"

    script:
    """
    vep -i $vcf -o ${vcf.simpleName}.vep.tsv --tab \\
        --assembly ${params.assembly} --cache --dir_cache ${params.vep_cache} --offline \\
        --everything --pick --af_gnomade --plugin CADD --plugin AlphaMissense \\
        --stats_file ${vcf.simpleName}.vep_summary.html --fork ${task.cpus}
    """
}