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

[aksenia]

Adds forced calling (--genotype-vcf) to the existing sniffles module, as suggested in the review of #13105. Sniffles genotypes a known set of structural variants in the same BAM/CRAM and writes the same --vcf output as regular calling, with the known SVs as one additional optional file.

• New 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. This changes the input of the module, so callers need to add an empty fourth element.
• A gzipped sites VCF is decompressed first, because Sniffles reads the file as plain text (Sniffles 2.8.1 bug with handling vcf.gz files fritzsedlazeck/Sniffles#613).
• Tests: the existing tests get the extra []; three new tests (gzipped sites VCF, plain sites VCF, stub) use the small HG002 ONT subset and known-SV VCF added in Add HG002 ONT SV genotyping test data test-datasets#2302. The test config uses the calling arguments only when no sites file is given.
• No existing long-read test data had a matching known-SV VCF at a depth where heterozygous and homozygous genotypes can be called (see add meta to bwa index #2302).

Replaces #13105.

Generated by Claude

PR checklist

Closes #13106

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[aksenia]

Hi @awgymer ! Is this what you had in mind for the extended module instead of the new one?