Version 0.3.0

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.

Version 0.2.3

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

Version 0.2.2

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

Version 0.2.1

0.2.1 - 2024/09/10

Changed

• Upgraded profile_dists to version 1.0.2 in the container closure

Version 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 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+.

Version 0.1.0

0.1.0 - 2024-06-28

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.