xlavir - Informative Excel reports from viral sequencing Nextflow analysis

Excel report from viral sequencing data analysis output from the nf-core/viralrecon or CFIA-NCFAD/nf-virontus Nextflow pipelines.

Usage

Create an Excel report from a Nextflow pipeline run:

# e.g. run nf-core/viralrecon Nextflow pipeline against SARS-CoV-2 samples
# sequenced by Illumina using the ARTIC V4.1 protocol
nextflow run nf-core/viralrecon \
  -profile docker \
  --input samplesheet.csv \
  --platform illumina \
  --protocol amplicon \
  --genome 'MN908947.3' \
  --primer_set artic \
  --primer_set_version '4.1' \
  --skip_assembly \
  --outdir viralrecon-results
# create Excel report from Nextflow pipeline run
xlavir viralrecon-results  xlavir-report-viralrecon-results.xlsx

See example report from test data in tests/data/tools.

Features

Collect sample results from a nf-core/viralrecon or CFIA-NCFAD/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) from the following variant callers
  - Bcftools
  - iVar
  - Medaka
  - Nanopolish
  - Clair3
- Consensus sequences
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)

License

Distributed under the terms of the MIT license, "xlavir" is free and open source software.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

Metadata

Release files for xlavir 1.0.3

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for xlavir 1.0.3
File	Size	Uploaded
xlavir-1.0.3.tar.gz	1.2 MB	Feb 17, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for xlavir 1.0.3
File	Interpreter	ABI	Platform	Reset
xlavir-1.0.3-py3-none-any.whl 35.2 kB Feb 17, 2026	Python 3	none	any	Details

Total release size: 1.3 MB

Release files / xlavir-1.0.3.tar.gz

Download URL	xlavir-1.0.3.tar.gz
Size	1.2 MB
Tags	Source
SHA-256 checksum How to use checksums	`451da660cd48daf80c89027649dc7496f7608fe8a540ba3e0a994c12dc58a676`
BLAKE2b-256 checksum How to use checksums	`532cac8d898d913f90d59e5187ef5a27ecd6cac3333d3880442c6272f4e4bc95`
Upload date	Feb 17, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.7`

Release files / xlavir-1.0.3-py3-none-any.whl

Download URL	xlavir-1.0.3-py3-none-any.whl
Size	35.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`4c0d2c4078e861112126bbf4a70cd9a146333aa013f14a5adeac93cfe589d03c`
BLAKE2b-256 checksum How to use checksums	`e279ef8410b6b5c075cb9f06d60b71b2e81ac25a4aae10f4e87090437a3fdcf2`
Upload date	Feb 17, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.1.0 CPython/3.13.7`