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
  • 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.