sniffles: add forced calling (--genotype-vcf) #13106

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Description

Sniffles can genotype a given set of structural variants in a long-read alignment (forced calling, --genotype-vcf). It uses the same --input BAM/CRAM and writes the same --vcf output as regular SV calling, with the known SVs as one additional optional file.

Proposal: add this to the existing sniffles module as an optional genotype_vcf in the first input tuple (tuple val(meta), path(input), path(index), path(genotype_vcf), [] for regular calling) and a --genotype-vcf argument built from it. A gzipped sites VCF is decompressed first, because Sniffles reads the file as plain text (fritzsedlazeck/Sniffles#613). Tests use the small HG002 ONT subset and known-SV VCF added in nf-core/test-datasets#2302.

This replaces the earlier proposal of a separate sniffles/genotypevcf module, after review feedback that the genotype mode belongs in the existing module.

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