* Collect sample results from a [nf-core/viralrecon] or [peterk87/nf-virontus] into an Excel report
* [Samtools] read mapping stats (`flagstat`)
* [Mosdepth] read mapping coverage information
* Variant calling information ([SnpEff] and [SnpSift] results, VCF file information)
* Consensus sequences
* [iVar] VCF parsing
* QA/QC of sample analysis results (basic PASS/FAIL based on minimum genome coverage and depth)
* Nextflow workflow execution information
* Prepend worksheets from other Excel documents into the report (e.g. cover page/sheet, sample sheet, lab results)
* Add custom images into worksheets with custom names and descriptions (e.g. phylogenetic tree figure PNG)
[nf-core/viralrecon]: https://github.com/nf-core/viralrecon
[peterk87/nf-virontus]: https://github.com/peterk87/nf-virontus/
[Bcftools]: https://www.htslib.org/doc/bcftools.html
[Samtools]: https://samtools.github.io/
[SnpEff]: https://pcingola.github.io/SnpEff/se_introduction/
[SnpSift]: https://pcingola.github.io/SnpEff/ss_introduction/
[Mosdepth]: https://github.com/brentp/mosdepth
[Medaka]: https://github.com/nanoporetech/medaka
[Longshot]: https://github.com/pjedge/longshot
[iVar]: https://andersen-lab.github.io/ivar/html/manualpage.html
[Clair3]: https://github.com/HKU-BAL/Clair3
[pysam]: https://pysam.readthedocs.io/en/latest/
[ruff]: https://github.com/charliermarsh/ruff
[flake8]: https://flake8.pycqa.org/en/latest/
[Nextclade]: https://clades.nextstrain.org/