epi2me-labs/wf-bacterial-genomes: v2.0.2

Published March 3, 2026 | Version v2.0.2

Software Open

Implemented fastlint to filter low complexity reads and improve Flye assembly performance.
- --fastlint_threshold parameter can be used to adjust DUST filter stringency.
- --run_fastlint can be used to disable DUST filtering step.

Updated to wf-template v5.7.1 to maintain compliance with our latest wf-template standard, changing:
- The README docs sections to move related protocols after inputs and outputs.
- Links in the README to point at our new documentation website.
- Our pre-commit configuration to resolve a dependency issue in our test infrastructure.

Resolved an issue causing Bakta annotations to fail in cloud runs.
- Updated the Docker container to include the "light" Bakta database.
- Removed the functionality that allowed the workflow to download an externally stored Bakta database, eliminating the need for an internet connection on first execution.
- Removed the --bakta_db_type parameter. To use the "full" Bakta database, it must be downloaded separately and provided to the workflow using the --bakta_db parameter.
Fixed an issue where stderr could be written to versions.txt, causing the workflow to crash.

Files

Name	Size	Download all
epi2me-labs/wf-bacterial-genomes-v2.0.2.zip md5:fd1e22ce39fd01d0bd383fae6a63f2fb	41.7 MB	Preview Download

Is supplement to: Software: https://github.com/epi2me-labs/wf-bacterial-genomes/tree/v2.0.2 (URL)