Excel report from viral sequencing analysis output
Project description
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
- 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
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