phac-nml/arboratornf: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

0.3.2 - 2025-01-15

Updated the build of the arborator container in order to update the genomic_address_service dependency to version 0.1.3, which fixes an issue with branch lengths in Newick files PR 27.

0.3.1 - 2024-11-05

Fixed the replacement of docker.userEmulation with docker.runOptions = '-u $(id -u):$(id -g)' that was causing a bug in Azure

0.3.0 - 2024-10-21

Added the ability to include a sample_name column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration.
- sample_name special characters 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
- Fixed linting issues in CI caused by nf-core 3.0.1

0.2.0 - 2024-09-05

Changed

Upgraded locidex/merge to version 0.2.3 and updated input_assure.py and test data for compatibility with the new mlst.json allele file format.
- PR19

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

0.1.0 - 2024-08-20

Initial release of the arboratornf pipeline to be used for running Arborator under Nextflow.

`Added`

Basic functionality of Arborator.
Added support for metadata.
Automatically generate Arborator config files.
ArborView integration.