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v1.2.1

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@ahmig ahmig released this 30 Jun 07:51
· 188 commits to main since this release
v1.2.1
a994c49

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

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