Metadata-Version: 2.4
Name: xlavir
Version: 1.0.3
Summary: Excel report from viral sequencing analysis output
Project-URL: Homepage, https://github.com/CFIA-NCFAD/xlavir
Project-URL: Repository, https://github.com/CFIA-NCFAD/xlavir.git
Project-URL: Bug Tracker, https://github.com/CFIA-NCFAD/xlavir/issues
Author-email: Peter Kruczkiewicz <peter.kruczkiewicz@gmail.com>
License: MIT License
        
        Copyright (c) 2021, Peter Kruczkiewicz
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
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        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        
License-File: LICENSE
Keywords: bioinformatics,excel report,nextflow,virus sequencing
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Unix Shell
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Requires-Python: >=3.8
Requires-Dist: beautifulsoup4
Requires-Dist: biopython
Requires-Dist: imageio
Requires-Dist: numpy>=1.20.0
Requires-Dist: odfpy
Requires-Dist: openpyxl
Requires-Dist: pandas
Requires-Dist: pydantic
Requires-Dist: pysam
Requires-Dist: rich
Requires-Dist: typer
Requires-Dist: xlsxwriter
Provides-Extra: dev
Requires-Dist: mypy; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Requires-Dist: twine; extra == 'dev'
Requires-Dist: wheel; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest-runner; extra == 'test'
Requires-Dist: pytest>=3; extra == 'test'
Description-Content-Type: text/markdown

# xlavir - Informative Excel reports from viral sequencing Nextflow analysis

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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:

```bash
# 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](xlavir-report.xlsx) 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.

[Cookiecutter]: https://github.com/audreyr/cookiecutter
[audreyr/cookiecutter-pypackage]: https://github.com/audreyr/cookiecutter-pypackage
[nf-core/viralrecon]: https://github.com/nf-core/viralrecon
[CFIA-NCFAD/nf-virontus]: https://github.com/CFIA-NCFAD/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
[MIT]: https://opensource.org/licenses/MIT
[Nextflow]: https://www.nextflow.io/
[iVar]: https://andersen-lab.github.io/ivar/html/
[Medaka]: https://github.com/nanoporetech/medaka
[Nanopolish]: https://github.com/jts/nanopolish/
[Clair3]: https://github.com/HKU-BAL/Clair3
