Skip to main content

Excel report from viral sequencing analysis output

Project description

xlavir - Informative Excel reports from viral sequencing Nextflow analysis

PyPI PyPI - Python Version PyPI - License PyPI - Downloads PyPI - Status CI

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
  • 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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

xlavir-1.0.2.tar.gz (1.2 MB view hashes)

Uploaded Source

Built Distribution

xlavir-1.0.2-py3-none-any.whl (34.9 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page