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phac-nml/gasnomenclature: Changelog

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

0.3.0 - 2025/01/09

Added

  • Enhanced the pipeline to integrate optional user-provided reference profiles and cluster addresses for additional samples PR #29:

    • Added support for --db_profiles via the APPEND_PROFILES process
    • Added support for --db_clusters via the APPEND_CLUSTERS process

  • Added tests to verify the additional databases can be incorporated and that both databases are required together for their respective processes.

  • Added the ability to include a sample_name column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration PR #30:

    • 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

  • Updated gas/call to version 0.1.2 and both CLUSTER_FILE and APPEND_CLUSTERS to comply with the latest formatting requirements.

Changed

  • Genomic Service Address version 0.1.1 -> 0.1.3

  • Refined the format of reference_cluster.tsv (rclusters) used by GAS CALL to require only id and address columns. This change involved updates to both the append_clusters and cluster_file modules.

0.2.3 - 2024/09/25

Changed

  • Updated FILTER_QUERY process to treat query_ids as a file input (path instead of val) for proper file path handling across environments PR27
  • Addressed Issue26

0.2.2 - 2024/09/13

Changed

  • Updated FILTER_QUERY to process query IDs from a file rather than passing them as a string, preventing errors caused by long argument strings PR24

0.2.1 - 2024/09/10

Changed

  • Upgraded profile_dists to version 1.0.2 in the container closure

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 PR20
  • Removed quay.io docker repository tags from modules PR19

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

0.1.0 - 2024/06/28

Initial release of the Genomic Address Nomenclature pipeline to be used to assign cluster addresses to samples based on an existing cluster designations.

Added

  • Input of cg/wgMLST allele calls produced from locidex.
  • Output of assigned cluster addresses for any query samples using profile_dists and gas call.