Replace param haplotypecaller_filter, haplotyper_filter and dnascope_filter with variant_filter

[asp8200]

Description of feature

No need to have three (or more) params for skipping the variant-filtering.

Replace the "options" haplotypecaller_filter, haplotyper_filter and dnascope_filter for --skip_tools with variant_filter

https://nfcore.slack.com/archives/C02MDBZAYJK/p1694010751853099

Also, add variant-filtering for mutect2.

[asp8200]

Might one want to run several variant-callers but only skip the variant-filter for some of them? Like

nextflow run nf-core/sarek <usual stuff> --tools haplotypecaller,sentieon_haplotyper --skip_tools haplotypecaller_filter

With a cmd like that the variant-filter could only be applied to the vcf from the GATK haplotypecaller and NOT to the vcf from the Sentieon Haplotyper. Do we need that kind of flexibility?

[asp8200]

Rike suggested that we keep haplotypecaller_filter, haplotyper_filter and dnascope_filter for --skip_tools as it adds some flexibility.