So according to this file: https://github.com/nf-core/raredisease/blob/master/subworkflows/local/annotate_mt_snvs.nf There are 14:

workflow ANNOTATE_MT_SNVS {
    take:
        ch_mt_vcf              // channel: [mandatory] [ val(meta), path(vcf) ]
        ch_mt_tbi              // channel: [mandatory] [ val(meta), path(tbi) ]
        ch_cadd_header         // channel: [mandatory] [ path(txt) ]
        ch_cadd_resources      // channel: [mandatory] [ path(annotation) ]
        ch_genome_fasta        // channel: [mandatory] [ val(meta), path(fasta) ]
        ch_vcfanno_extra       // channel: [mandatory] [ [path(vcf),path(index)] ]
        ch_vcfanno_lua         // channel: [mandatory] [ path(lua) ]
        ch_vcfanno_resources   // channel: [mandatory] [ [path(vcf1),path(index1),...,path(vcfn),path(indexn)] ]
        ch_vcfanno_toml        // channel: [mandatory] [ path(toml) ]
        val_vep_genome         // string:  [mandatory] GRCh37 or GRCh38
        val_vep_cache_version  // string:  [mandatory] 107
        ch_vep_cache           // channel: [mandatory] [ path(cache) ]
        ch_vep_cache           // channel: [mandatory] [ path(cache) ]
        ch_vep_extra_files     // channel: [mandatory] [ path(files) ]

But one is dupliated:

ch_vep_cache