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Automatically update SARS-CoV-2 datasets.

This requires scientific review. Once this PR is merged to master, the data will be available on master.clades.nextstrain.org and for Nextclade CLI with --dataset-server=https://data.master.clades.nextstrain.org.

Like usual, the manual fast-forward of release branch to master branch is needed if you want these changes to be released, to appear on clades.nextstrain.org and be available for Nextclade CLI.

Here are some links to facilitate the review:

Tree on Nextstrain.org Submitted dataset Nextclade link¹
staging/nextclade/sars-cov-2 nextstrain/sars-cov-2/wuhan-hu-1/orfs nextstrain/sars-cov-2/wuhan-hu-1/orfs
staging/nextclade/sars-cov-2/nsp nextstrain/sars-cov-2/wuhan-hu-1/proteins nextstrain/sars-cov-2/wuhan-hu-1/proteins
staging/nextclade/sars-cov-2/BA.2.86 nextstrain/sars-cov-2/BA.2.86 nextstrain/sars-cov-2/BA.2.86

¹ - Please make sure to wait for the CI to deploy dataset server before using links in the "Nextclade link" column. Once you see the "chore: rebuild [skip ci]" commit from nextstrain-bot below the links are ready to go. Otherwise they display the previous data (from master branch).


Note: this pull request is submitted automatically. See: .github/workflows/update-sars-cov-2-datasets.yml.


⚠️ WARNING: do not push any changes to this branch (auto-update-sc2-datasets). The branch can be deleted or overwritten by the automation. If you want to add changes, create a new branch based on this branch and push there instead.

@github-actions github-actions bot closed this Dec 22, 2025
@github-actions github-actions bot deleted the auto-update-sc2-datasets branch December 22, 2025 21:24
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