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CHANGELOG

We use this CHANGELOG to document breaking changes, new features, bug fixes, and config value changes that may affect both the usage of the workflows and the outputs of the workflows.

Changes for this project do not currently follow the Semantic Versioning rules. Instead, changes appear below grouped by the date they were added to the workflow.

2026

  • TBD: Optimized thread usage for augur subsample. #109
  • 25 February 2026: Changes to files referenced in subsample config will trigger a re-run of the rule. #90
  • 25 February 2026: Changes to non-subsampling config will no longer trigger a re-run starting from subsampling. #91
  • 09 February 2026: MAJOR CHANGES Switched ingest outputs to separate OPEN vs RESTRICTED files. The phylogenetic workflow inputs have been updated to reflect this change. The default build has been updated to only include OPEN data. Please see phylogenetic/README.md for details on how to use the RESTRICTED data. #108
  • 09 February 2026: MAJOR CHANGES Added multiple input support to phylogenetic workflow, please see phylogenetic/README.md for more details. #107
  • 23 January 2026: Restored support for nextstrain run, which was broken when adding dynamic colors generation. #105
  • 22 January 2026: ingest: fixed the uploaded sequences file extension so the file at https://data.nextstrain.org/files/workflows/measles/sequences.fasta.zst is properly updated. #103
  • 21 January 2026: ingest: switched strain back to the original isolate names. #98
  • 15 January 2026: phylogenetic: Split subsampling into early and late sampling groups 530da56
  • 14 January 2026: MAJOR CHANGES in phylogenetic workflow 1cf1299...0313508
    • increased number of sequences to include in genome build
    • added geographic trait reconstruction for genome build. Requires new config params traits.columns and traits.sampling_bias_correction
    • added dynamic colors generation
  • 09 January 2026: MAJOR CHANGES - Switched to Pathoplexus as the data source for the ingest and phylogenetic workflows. Please consult the Pathoplexus Data Use Terms for details on how the data can be used. #95

2025

  • 22 December 2025: Added workflow for creating the genome Nextclade dataset. #65
  • 30 September 2025: The 'gene' wildcard was renamed as 'build', and is now a config key rather than a declaration in the phylogenetic snakefile.
  • 29 September 2025: Restored support for nextstrain run, which was broken in the switch the augur subsample. #73
  • 26 September 2025: Updated workflow compatibility declaration in nextstrain-pathogen.yaml. This requires Nextstrain CLI >=10.3.0 to setup and update the pathogen without error messages. However, workflows will still run with Nextstrain CLI <10.3.0 #69
  • 24 September 2025: Implemented augur subsample, replacing augur filter steps for both genome and N450 workflows. This is a breaking change. #70
    • Replaces augur filter calls with augur subsample.
    • Replaces filter and filter_N450 with subsample section in the config.yaml.
  • 24 September 2025: Configuration resolved at run time is now written to results/run_config.yaml. #70
  • 22 September 2025: Fixed a bug where rule align would fail when the reference sequence was present in the output of rule filter #68
  • 4 June 2025: Vendored nextstrain/shared to parse config paths across workflows #62
  • 21 May 2025: ingest - Replace various scripts with new augur curate commands #61
    • Replaces ncov-ingest geolocation rules with built-in augur curate geolocation rules
    • Requires a new curate.genbank_location_field config param.
    • The config param curate.geolocation_rules_url is no longer supported
  • 28 March 2025: Added support for nextstrain run across all workflows #55
  • 20 March 2025: phylogenetic - Add division to geo-resolutions and coloring #59

2024

  • 6 November 2024: phylogenetic - Fix "translate" and "export" rules to use references from config #53
  • 19 September 2024: ingest - config nextclade.field_map accepts key-value pairs #52
  • 3 July 2024: phylogenetic - Add frequencies panel for N450 build #42
  • 28 June 2024: phylogenetic - Add default description for builds #41
  • 7 June 2024: Assign genotypes using Nextclade dataset and visualize on tree PR #36
  • 9 May 2024: Create a N450 tree that can be used as part of a Nextclade dataset to assign genotypes to measles samples based on criteria outlined by the WHO PR #28
  • 25 April 2024: Add specific sequences and metadata to the measles trees, including WHO reference sequences, vaccine strains, and genotypes reported on NCBI PR #26
  • 10 April 2024: Add a single GH Action workflow to automate the ingest and phylogenetic workflows PR #22
  • 2 April 2024: Add nextstrain-automation build-configs for deploying the final Auspice dataset of the phylogenetic workflow PR #21
  • 1 April 2024: Create a "N450" tree using the 450 nucleotides encoding the carboxyl-terminal 150 amino acids of the nucleoprotein, which is highly represented on NCBI for measles. PR #20
  • 15 March 2024: Connect ingest and phylogenetic workflows to follow the pathogen-repo-guide by uploading ingest output to S3, downloading ingest output from S3 to phylogenetic directory, using "accession" column as the ID column, and using a color scheme that matches the new region name format. PR #19
  • 1 March 2024: Add phylogenetic directory to follow the pathogen-repo-guide, and update the CI workflow to match the new file structure. PR #18
  • 14 February 2024: Add ingest directory from pathogen-repo-guide and make measles-specific modifications. PR #10
  • 11 January 2024: Use a config file to define hardcoded parameters and file paths, and add a change log. PR #9