| Name | xlavir JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | |
| Summary | Excel report from viral sequencing analysis output |
| upload_time | 2023-11-28 23:38:12 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| 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. |
| keywords |
bioinformatics
excel report
nextflow
virus sequencing
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# xlavir - Informative Excel reports from viral sequencing Nextflow analysis
[](https://pypi.python.org/pypi/xlavir)
[](https://pypi.python.org/pypi/xlavir)
[](https://pypi.python.org/pypi/xlavir)
[](https://pypi.python.org/pypi/xlavir)
[](https://pypi.python.org/pypi/xlavir)
[](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
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"description": "# xlavir - Informative Excel reports from viral sequencing Nextflow analysis\n\n[](https://pypi.python.org/pypi/xlavir)\n[](https://pypi.python.org/pypi/xlavir)\n[](https://pypi.python.org/pypi/xlavir)\n[](https://pypi.python.org/pypi/xlavir)\n[](https://pypi.python.org/pypi/xlavir)\n[](https://github.com/peterk87/xlavir/actions)\n\nExcel report from viral sequencing data analysis output from the\n[nf-core/viralrecon] or [CFIA-NCFAD/nf-virontus] [Nextflow] pipelines.\n\n## Usage\n\nCreate an Excel report from a Nextflow pipeline run:\n\n```bash\n# e.g. run nf-core/viralrecon Nextflow pipeline against SARS-CoV-2 samples\n# sequenced by Illumina using the ARTIC V4.1 protocol\nnextflow run nf-core/viralrecon \\\n -profile docker \\\n --input samplesheet.csv \\\n --platform illumina \\\n --protocol amplicon \\\n --genome 'MN908947.3' \\\n --primer_set artic \\\n --primer_set_version '4.1' \\\n --skip_assembly \\\n --outdir viralrecon-results\n# create Excel report from Nextflow pipeline run\nxlavir viralrecon-results xlavir-report-viralrecon-results.xlsx\n```\n\nSee [example report](xlavir-report.xlsx) from test data in `tests/data/tools`.\n\n## Features\n\n* Collect sample results from a [nf-core/viralrecon] or\n [CFIA-NCFAD/nf-virontus] into an Excel report\n * [Samtools] read mapping stats (`flagstat`)\n * [Mosdepth] read mapping coverage information\n * Variant calling information ([SnpEff] and [SnpSift] results, VCF file\n information) from the following variant callers\n * [Bcftools]\n * [iVar]\n * [Medaka]\n * [Nanopolish]\n * [Clair3]\n * Consensus sequences\n* QA/QC of sample analysis results (basic PASS/FAIL based on minimum genome\n coverage and depth)\n* [Nextflow] workflow execution information\n* Prepend worksheets from other Excel documents into the report (e.g. cover\n page/sheet, sample sheet, lab results)\n* Add custom images into worksheets with custom names and descriptions (e.g.\n phylogenetic tree figure PNG)\n\n## License\n\nDistributed under the terms of the [MIT] license, \"xlavir\" is free and open\nsource software.\n\n## Credits\n\nThis package was created with [Cookiecutter] and the\n[audreyr/cookiecutter-pypackage] project template.\n\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[audreyr/cookiecutter-pypackage]: https://github.com/audreyr/cookiecutter-pypackage\n[nf-core/viralrecon]: https://github.com/nf-core/viralrecon\n[CFIA-NCFAD/nf-virontus]: https://github.com/CFIA-NCFAD/nf-virontus/\n[Bcftools]: https://www.htslib.org/doc/bcftools.html\n[Samtools]: https://samtools.github.io/\n[SnpEff]: https://pcingola.github.io/SnpEff/se_introduction/\n[SnpSift]: https://pcingola.github.io/SnpEff/ss_introduction/\n[Mosdepth]: https://github.com/brentp/mosdepth\n[MIT]: https://opensource.org/licenses/MIT\n[Nextflow]: https://www.nextflow.io/\n[iVar]: https://andersen-lab.github.io/ivar/html/\n[Medaka]: https://github.com/nanoporetech/medaka\n[Nanopolish]: https://github.com/jts/nanopolish/\n[Clair3]: https://github.com/HKU-BAL/Clair3\n",
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