0.3.1

0.3.1 - 2024-11-05

CHANGED

• Fixed the replacement of docker.userEmulation with docker.runOptions = '-u $(id -u):$(id -g)' that was causing a bug in Azure.
• Modified documentation (missed in 0.3.0 release)

0.3.0

0.3.0 - 2024-10-21

ADDED

• Modified the template for input csv file to include a sample_name column in addition to sample in-line with changes to IRIDA-Next update as seen with the speciesabundance pipeline. (PR 23)

  • 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

CHANGED

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

0.2.0

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

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.