v1.3.1

1.3.1 (2025-11-24)

Bug Fixes

• force reading VCF fields as character (18e5004)

v1.3.0

Features

• Decouple report plots (context phylogeny, diversity, allele frequency trajectories, dN/dS, demix, heatmap) from input data and parameterize plot sizes, palettes, and shapes.
• Replace distance calculation Python script with lightweight afwdist for faster allele frequency-weighted distances.
• Upgrade Freyja to v2.0.1 (adds limit solver threads for demixing) and add barcode timestamps to the report.
• Add seed params to IQ-TREE rules for deterministic phylogenetic inference.
• Extract SARS-CoV-2 feature coordinates directly from GenBank and use GenBank qualifiers for annotations.
• Extract and standardize VCF fields and variant annotations using SnpEff/SnpSift.
• Parallelize sample variant processing and filtering and update variant calling thread directives.

Bug fixes

• Correct variant table merging, column names, and duplicates in VCF fields.
• Handle SnpEff error/warning messages correctly and avoid empty columns causing parsing failures.
• Fix dN/dS feature extraction via GenBank file usage.
• Fix plot errors for zero variants or missing data.
• Fix context phylogeny legend and class rendering issues.
• Adjust variant calling and demixing CPU settings to prevent unexpectedly high usage.
• Correct input/output paths, sample name detection, and minor typos.

Documentation and code formatting

• Document SnpEff config fields and new GB_FEATURES key (moves feature lists from JSON to config YAML file).
• Update report CSS and switch font to Noto Sans.
• Clarify input descriptions and add short tl;dr instructions.
• Run Quarto from the command line with updated environment handling.
• Remove unused dependencies and scripts and reduce unnecessary R tidyverse package loading.
• Standardize rule naming and results column types.
• Minor wording and format improvements.

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Full Changelog: v1.2.2...v1.3.0

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 report rule shell directive
• Update CI badge layout

Full Changelog: v1.2.1...v1.2.2

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: v1.2.0...v1.2.1

v1.2.0

• Containerize workflow (hosted image via the included Dockerfile)
• Extend workflow documentation (config/README.md)
• Cosmetic improvements

Full Changelog: v1.1.0...v1.2.0

v1.1.0

• Reorder report section
• Update instructions for HPC environments
• Cosmetic improvements

Full Changelog: v1.0.0...v1.1.0

v1.0.0

First public release of VIPERA.