Download Nextclade TSV from S3

nextstrain / flu_frequencies

Flu clade and mutation frequencies

https://flu-frequencies.vercel.app

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Download Nextclade TSV from S3 #38

Closed huddlej closed 5 months ago

huddlej commented 5 months ago

Description of proposed changes

Instead of running Nextclade on all sequences per lineage, download Nextclade TSVs from S3 where they have been uploaded as part of the corresponding seasonal-flu repo's GitHub Action [1]. With this change, frequency estimation for all flu lineages takes less than 1 minute on 8 CPUs.

[1] https://github.com/nextstrain/seasonal-flu/actions/workflows/run-nextclade.yaml

Checklist

[x] Tested locally
[x] Checks pass

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Name	Status	Preview	Updated (UTC)
flu-frequencies	✅ Ready (Inspect)	Visit Preview	May 13, 2024 8:37pm