v2.9.1

Update: Please be aware that the first build (0) of this release had a wrong version string in the code. So if you see "v2.8.2", you might actually be running v2.9.1. From build 1, this is fixed.

Full Changelog: v2.8.2...v2.9.1

2.9.1

• Breaking change: new passthrough parameter system rolled out to most rules.
• Update cite value to reflect preprint doi https://doi.org/10.1101/2024.07.12.603264
• Add more tools to passthrough argument feature. And write documentation.
• Fixed an error that meant that panaroo was using the Prokka annotation (.gff) regardless of the annotator being set with --config annotator=[bakta|prokka].
• Fixed an error that meant that both Bakta and Prokka would run even though the user had selected one with --config annotator=[bakta|prokka]. Thanks to @michoug
• Minor fixes.