Version 0.3.0

0.3.0 - 2024-09-10

Changed

• Upgraded profile_dist container to version 1.0.2
• Upgraded locidex/merge to version 0.2.3 and updated input_assure and test data for compatibility with the new mlst.json allele file format.
  • PR28
• Aligned container registry handling in configuration files and modules with phac-nml/pipeline-standards
  • PR28

This pipeline is now compatible only with output generated by Locidex v0.2.3+ and Mikrokondo v0.4.0+.

Version 0.2.0

0.2.0 - 2024-06-26

Added

• Support for mismatched IDs between the samplesheet ID and the ID listed in the corresponding allele file.

Changed

• Updated ArborView to v0.0.7-rc1.

Fixed

• The scaled distance thresholds provided when using --pd_distm scaled and --gm_thresholds are now correctly understood as percentages in the range [0.0, 100.0].

Version 0.1.0

0.1.0 - 2024-05-28

Initial release of the Genomic Address Service Clustering pipeline to be used for distance-based clustering of cg/wgMLST data.

Added

• Input of cg/wgMLST allele calls produced from locidex.
• Output of a dendrogram, cluster codes, and visualization using profile_dists, gas mcluster, and ArborView.