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v0.2.3-beta: Performance Optimization and Checkpoint Reliability

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@qianxuans qianxuans released this 24 Dec 00:20
· 54 commits to main since this release
v0.2.3-beta
d6359b1

THRESHER v0.2.3-beta

This release focuses on performance optimization and workflow reliability

Major Changes

  • Native Snakemake Parallelization: Migrated from GNU parallel to Snakemake's built-in parallelization for bakta, mummer4, blastx rules and so on. This enables efficient checkpointing and resume functionality. Interrupted runs now resume per-genome rather than restarting entire steps from scratch.

  • WhatsGNU Database Optimization: Changed WhatsGNU rule to load the database once instead of repeatedly per genome, improving analysis speed for large datasets.

  • Edge Case Fixes: Resolved various minor issues where certain edge cases would cause pipeline failures.

Known Issues

  • Input genomes that are not the expected species may cause errors. A fix is actively in development.

Notes

  • This is a beta release - please report any issues on the GitHub issue tracker
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