Excel report from viral sequencing analysis output
Project description
xlavir
Excel report from viral sequencing data analysis output from the nf-core/viralrecon or peterk87/nf-virontus Nextflow pipelines.
Free software: MIT license
Documentation: https://xlavir.readthedocs.io.
Features
- Collect sample results from a nf-core/viralrecon or peterk87/nf-virontus into a 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)
Roadmap
Bcftools variant calling stats sheet
Sample metadata table to merge with certain stats?
YAML config to info sheet?
coverage chart with controls?
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.5.0 (2021-07-30)
Added support for Nanopolish VCF parsing as generated by the ARTIC pipeline
Added deduplication of VCF and SnpSift entries since the ARTIC pipeline may produce VCF files with duplicate variant calls due to overlap between amplicons.
Added VCF and SnpSift test data for CLI test to generate Excel report.
0.4.3 (2021-07-29)
Fix an issue where single base positions are being reported as 0-based when all other ranges are 1-based for reporting of low/no coverage regions from Mosdepth per-base BED files (#10).
0.4.2 (2021-05-21)
Add support for nf-core/viralrecon version 2.0 (requires Mosdepth bed.gz files be output; needs custom modules.config like this one)
Nextclade CLI per sample results parsed into sheet showing useful info like Nextstrain clade, # of mutations, # of PCR primer changes
Added check that input directory exists and is a directory
Added sheet with xlavir info
Added Gene, Variant Effect, Variant Impact, Amino Acid Change to Variant Summary table
0.4.1 (2021-05-14)
Add reference sequence length to QC stats table. Get ref seq length from max mosdepth per base BED coverage value.
Add more conditional formatting
Fix execution_report.html finding
Fix version printing; add to help
Add epilog with usage info
0.4.0 (2021-04-23)
Adds “Variants Summary” sheet summarizing variant information across all samples
Adds comments to AF values in “Variant Matrix” sheet
Fixes width/height of cell comments to be based on length of comment text
0.3.0 (2021-04-23)
Adds support for adding Ct values from a Ct values table (tab-delimited, CSV, ODS, XLSX format) into an xlavir report.
0.2.4 (2021-04-19)
Fixes issue with SnpSift table file parsing and variable naming in variants.py (#4, #5)
0.2.3 (2021-04-19)
Fixes issue with SnpSift table file parsing. Adds check to see if SnpSift column is dtype object/str before using .str Series methods (#4)
0.2.2 (2021-03-30)
Fixes issue with SnpEff/SnpSift AA change parsing.
0.2.1 (2021-03-29)
Fix division by zero error due to variants with DP values of 0
0.2.0 (2021-03-04)
0.1.1 (2021-02-16)
- Collect sample results from a nf-core/viralrecon or peterk87/nf-virontus into a Excel report
iVar VCF parsing
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)
Project details
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