Recent Releases of vipera
vipera - v1.2.2
Features
- Allow selection of alternate correlation method (Pearson, Spearman, Kendall) and exact‑p‑value option
- Add CI workflow to test the containerized Snakemake pipeline with Apptainer
- Automatically build and push Docker images on tagged releases
- Update R environment and container definitions
Bug fixes
- Suppress initial input‑function messages for cleaner logs for Snakemake v9+
- Remove duplicate legends on M-L tree
- Update p‑value extraction in SNP description reports to reflect the model output
Documentation and code formatting
- Clarify GISAID EpiCoV access caveats and workarounds in the context‑dataset docs
- Rename and update SLURM profile examples for compatibility with Snakemake v8+
- Improve style of the
reportruleshelldirective - Update CI badge layout
Full Changelog: https://github.com/PathoGenOmics-Lab/VIPERA/compare/v1.2.1...v1.2.2
- Python
Published by ahmig 7 months ago
vipera - v1.2.1
Features
- Add explicit support for Snakemake versions 8 and 9 and create separate test actions for Snakemake versions 7-9
- Add option to use BIONJ instead of NJ for distance tree construction
- Include the number of target samples in the phylogenetic clade and the distance tree method in report
- Expose maximum alternate allele frequency as a configurable parameter
- Allow usage of a local VCF file for masked positions
- Rename NSP configuration variables and annotation columns for extensibility
- Apply consistent formatting to R scripts and report rules
- Improve modularization with a separate Snakefile for core submodules
Bug fixes
- Fix handling of empty VCF files
- Avoid potential off-by-one in minimum context size checkpoint
- Correct zero-filling of alternate allele frequencies
- Fix calculation of percentage of tips in clades
- Resolve GitHub Actions dependency errors
- Update pandas and ggplot deprecated arguments
- Improve error message clarity and consistency
- Ensure all messages are logged and add Snakemake logs to GitHub artifacts
Documentation and code formatting
- Simplify and update
README.md - Update input metadata descriptions in
config/README.md
Special thanks to Zenggang Li and Brett Etchebarne at Michigan State University for taking an interest in the project and helping surface some of the issues that have now been addressed.
Full Changelog: https://github.com/PathoGenOmics-Lab/VIPERA/compare/v1.2.0...v1.2.1
- Python
Published by ahmig 8 months ago
vipera - v1.2.0
- Containerize workflow (hosted image and Dockerfile)
- Extend workflow documentation (config/README.md)
- Cosmetic improvements
Full Changelog: https://github.com/PathoGenOmics-Lab/VIPERA/compare/v1.1.0...v1.2.0
- Python
Published by ahmig about 2 years ago