Feat/add optional filter params

[krbe9202]

Add optional parameters for SV/SNV filtering and calling configuration

This PR adds seven new optional parameters that expose commonly needed filtering and calling controls as pipeline parameters, rather than requiring users to override module configs
locally.

New parameters

Parameter	Default	Description
filter_expansionhunter_htt	false	Filter HTT (Huntington) records from ExpansionHunter output
filter_sv_to_manta	false	Exclude TIDDIT from SVDB_MERGE keeping only Manta SVs
skip_vep_sv	false	Skip VEP annotation of SVs; SVDB_QUERY still runs
sv_size_threshold	null	Filter SVs larger than this value in bp (e.g. 1000000); null = no size filter
sv_freq_filter_expression	null	bcftools -e expression for SV frequency filtering (e.g. INFO/SWEFRQ >= 0.02)
manta_call_regions	null	BED.gz file restricting Manta to specific regions; null = whole genome (including decoy)
ml_prob_threshold	null	ML_PROB threshold for Sentieon DNAscope; null = use Sentieon's own MLrejected flag

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Ensure the test suite passes (nextflow run . -profile test_singleton,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

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