Xlavir

* Fix issue with PyPI installation

* Added support for [Bcftools][] and [Clair3][] VCFs
* Added support for getting depth info from BAM files with [pysam][]
* Ct column no longer added to Stats/QC sheet if no Ct info provided
* Added [ruff][] for linting, replacing [flake8][]
* Fixed issue with not all [Nextclade][] columns being included in Excel report
* Migrated to `pyproject.toml` from `setup.py`; removed files associated with legacy `setup.py` approach
* Migrated to Markdown from RST for README and CHANGELOG
* Removed `docs/` directory
* Added issue template forms
* Updated GitHub Actions CI workflow

Fixes sample name extraction from [nf-core/viralrecon][] [Medaka][] VCF
filename with ".merged" to get sample name that matches [SnpSift][] filename
extracted sample name.

* Added more checks for Medaka VCFs from low coverage samples which may produce ValueError and ZeroDivisionError errors

* Add support for reading annotated Medaka VCF files (`medaka_variant` VCF annotated with `medaka tools annotate`)
* Changed mutation string format to `{gene}:{AA change} ({NT change}{extra})` if there is an AA change
* Added low coverage filtering of variants for Medaka VCF
* "Variants Summary" table now sorted by nucleotide position

* Fixed shorter consensus sequences not being written to report
* Improve nf-virontus VCF compatibility