Remove stale emerging_lineage, immune_escape, and ace2_binding colorings#1213
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joverlee521
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Jun 30, 2026
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Seems reasonable to remove the outdated colorings, this opens the door to cleaning up ncov-ingest (nextstrain/ncov-ingest#504) as well.
| - 29 July 2025: Improved performance of calls to `augur filter`. This requires a minimum Augur version of 31.3.0. [PR 1178](https://github.com/nextstrain/ncov/pull/1178) | ||
| - 28 January 2026: Large JSON files are now automatically minified. This requires a minimum Augur version of 33.0.0. [PR 1194](https://github.com/nextstrain/ncov/pull/1194) | ||
| - 30 January 2026: Simplified code for reading metadata. This requires a minimum Augur version of 32.1.0. [PR 1195](https://github.com/nextstrain/ncov/pull/1195) | ||
| - 26 June 2026: Remove the stale `emerging_lineage`, `immune_escape`, and `ace2_binding` colorings. The latter two were computed from BA.2 deep-mutational-scanning data and are no longer accurate against current strains. [PR 1213](https://github.com/nextstrain/ncov/pull/1213) |
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I would also flag that the files.emerging_lineages config param has been removed.
This is technically a backwards incompatible change that warrants a new release. Perhaps batch all of the clean up PRs into a singe v18 release.
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Yeah, batching as v18 makes sense. We can merge these to master right and then tag master as v18?
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I added
along with the now-unused
files.emerging_lineagesconfig parameter
to the changelog
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yes, merge and then create a new release as per checklist
ncov/.github/pull_request_template.md
Lines 16 to 22 in f9c1522
These three Auspice colorings are no longer useful:
- emerging_lineage: the curated defaults/emerging_lineages.tsv list has not been
maintained and won't be revived.
- immune_escape / ace2_binding: computed from deep-mutational-scanning data against
BA.2, so they are inaccurate ("vs BA.2") against today's circulating strains.
emerging_lineage had real build machinery, all removed: the emerging_lineages rule
(augur clades over emerging_lineages.tsv) and its node-data wiring in
main_workflow.smk, the files.emerging_lineages config key, defaults/emerging_lineages.tsv
itself, the coloring + filter in both defaults/auspice_config.json and the dynamic
auspice_config rule in export_for_nextstrain.smk, the 18 emerging_lineage rows in
color_ordering.tsv, and the config-reference docs section.
immune_escape / ace2_binding are not produced by any rule here (the default
sars-cov-2 Nextclade dataset doesn't emit them; they came from the 21L DMS dataset /
upstream metadata). Removal is display-only: the two coloring blocks in both auspice
configs, plus their now-inert passthrough rename mappings in
scripts/join-metadata-and-clades.py.
A CI dry-run drops from 37 to 36 jobs (only the emerging_lineages rule) with no
errors, and defaults/auspice_config.json remains valid JSON.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Removes three Auspice colorings that are no longer useful.
Motivation
emerging_lineage— the curateddefaults/emerging_lineages.tsvlist hasn't been maintained and won't be revived.immune_escape/ace2_binding— computed from deep-mutational-scanning data against BA.2, so the "vs BA.2" colorings are inaccurate against today's circulating strains.What's removed
emerging_lineagehad real build machinery, all removed:rule emerging_lineages(anaugur cladesrun) + its node-data wiring inmain_workflow.smkfiles.emerging_lineagesconfig key indefaults/parameters.yamldefaults/emerging_lineages.tsv(now orphaned)defaults/auspice_config.jsonand the dynamicauspice_configrule inexport_for_nextstrain.smkemerging_lineagerows indefaults/color_ordering.tsvimmune_escape/ace2_bindingare not produced by any rule here (the defaultsars-cov-2Nextclade dataset doesn't emit them; they came from the 21L DMS dataset / upstream metadata), so removal is display-only:scripts/join-metadata-and-clades.pyVerification
grepforemerging_lineage|immune_escape|ace2_bindingacross the repo (excl. historical changelog) returns zero hits.defaults/auspice_config.jsonremains valid JSON (23 colorings / 9 filters, down from 26 / 10).snakemake --profile nextstrain_profiles/nextstrain-ci -nresolves with 36 jobs, down from 37 (only theemerging_lineagesrule), no errors.Test plan
colorings/filtersno longer contain the three keys.🤖 Generated with Claude Code