0.9.1

This release enables to pass assembled genomes to GABI, as an alternative to raw reads. This will enable users to analyse assemblies from e.g. external sources with the same tool chain as their in-house assembled genomes.

Other changes include:

• Removal of Mash in favour of Sourmash
• Switching to Sourmash for assigning taxonomic information to samples (previous, Kraken was used on raw reads)
• Adding a few on/off switches to allows users to selectively deactivate processing chains.
• Switching to a more comprehensive sourmash database to allow better matches to be found

This release again requires a re-install of the references.

0.9

Nearing a full release.

• Includes minor cosmetic fixes
• Adds sourmash over mash, including installation procedure.

This release requires a re-install of the references to include the Sourmash DB

0.8.1

Updated reporting schema, and some new tools.
Added new validation process to highlight problematic samples.

0.7

Release 0.7 adds:

• ConfindR metrics in platform-specific MultiQC reports
• Per-sample ConfindR metrics in the general summary report
• Upgrades ConfindR to 0.8.1

0.5

Updating cgMLST workflow, adding various warnings and allow users to permanently fail samples that do not meet certain minumum criteria.

0.4

This is a development release.

• Updating mob_suite to 3.1.8
• Updating pyMLST to 2.1.6
• Adding Chewbbaca Evaluate to generate HTML reports
• Cleaning up documentation
• Adding support or Apptainer
• Some updates to the documentation
• Adding a summary JSON report per sample