Based on #2043 

This PR adds optional VCF filtering functionality to the post-variant
calling workflow, enabling users to filter variant calls
from all variant callers using `bcftools view`. Additionally, it
refactors the post-variant calling logic to handle implicit
index creation and improve handling of variant callers that produce
multiple outputs.

 **Why These Changes**

1. Streamlines the workflow by providing PASS-filtered variants directly
  2. Maintains flexibility through customizable filtering criteria
3. Integrates seamlessly with existing normalization and concatenation
steps
4. Improves handling of variant callers with complex output structures
(e.g., Strelka, Manta)

  **New Filtering Feature**
- Adds --filter_vcfs parameter to enable optional VCF filtering with
`bcftools view` with default PASS filter
- Supports custom filtering criteria through
`--bcftools_filter_criteria` parameter
- Publishes filtered VCFs to variant_calling/filtered/<sample>/
<sample>.<variantcaller>.bcftools_filtered.vcf.gz

  **Workflow Refactoring**
- Makes index computation implicit for all bcftools operations,
simplifying channel handling
- Updates emit channel structure to properly account for implicit index
creation (.tbi/.csi)
- Uses basename consistently to handle variant callers that produce
multiple outputs
- Fixes channel wiring between filtering, normalization, and
concatenation steps
  - Removes unnecessary explicit tabix indexing process
  - Fix output structure in docs
  
  **Testing & CI**
  - Adds filtering tests for multiple variant callers
  - Enables filtering on full-size test profiles
  - Fixes FreeBayes filtered output publishing
  - Updates snapshots to reflect new output structure
  
  **Documentation**
  - Updates docs/output.md with new filtering section
  - Updates subway map diagrams to reflect new workflow

<!--
# nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not
relevant).
These are the most common things requested on pull requests (PRs).

Remember that PRs should be made against the dev branch, unless you're
preparing a pipeline release.

Learn more about contributing:
[CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-->

## 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](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/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>`).
- [ ] 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).