Version 0.4.1

0.4.1 - 2024-12-23

Changed

• Updated the version of GAS container 0.1.1 -> 0.1.3 used by gasclustering.

Version 0.4.0

0.4.0 - 2024-11-07

Changed

• Added the ability to include a sample_name column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration. (PR #31)

  • sample_name special characters (non-alphanumeric with exception of "_" and ".") will be replaced with "_"
  • If no sample_name is supplied in the column sample will be used
  • To avoid repeat values for sample_name all sample_name values will be suffixed with the unique sample value from the input file

Bug fix

• Fixed linting issues in CI caused by nf-core 3.0.1

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.