Metadata-Version: 2.1
Name: xlavir
Version: 1.0.2
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
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        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
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        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

[![PyPI](https://img.shields.io/pypi/v/xlavir.svg)](https://pypi.python.org/pypi/xlavir)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/xlavir.svg)](https://pypi.python.org/pypi/xlavir)
[![PyPI - License](https://img.shields.io/pypi/l/xlavir.svg)](https://pypi.python.org/pypi/xlavir)
[![PyPI - Downloads](https://img.shields.io/pypi/dm/xlavir.svg)](https://pypi.python.org/pypi/xlavir)
[![PyPI - Status](https://img.shields.io/pypi/status/xlavir.svg)](https://pypi.python.org/pypi/xlavir)
[![CI](https://github.com/peterk87/xlavir/workflows/CI/badge.svg?branch=master)](https://github.com/peterk87/xlavir/actions)

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
