phylogenetic: Use inline root sequence #42
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Based on feedback from @jameshadfield in nextstrain/zika#56 (comment) Looking at the existing dataset files on S3, the 5-6 KiB root-sequence.jsons are pretty negligible when the main Auspice JSONs are 600-800 KiB. Nextstrain datasets are limited by the 500MB memory cap in Chrome,¹ so we'd be fine adding the root sequence inline. This ensures that our uploads will include the root sequence so that they don't get out-of-sync with the main Auspice JSON. ¹ nextstrain/auspice#1622
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Merging since the CI run's outputs include root_sequence in the Auspice JSONs and the datasets looks good in auspice.us |
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Manually deleted cache and triggered a re-run of the ingest-to-phylo workflow. Once complete
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Removed the following files from s3://nextstrain-data/
Left the E gene root-sequence.json files since they are not being updated by this PR. |
j23414
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Apr 16, 2024
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Description of proposed changes
Explicitly state that the root-sequence.json file is an expected output of the core phylogenetic workflow.This also ensures that the Nextstrain automation ruledeploy_allwill include the root-sequence.json in the upload.Based on feedback from @jameshadfield in
nextstrain/zika#56 (comment)
Looking at the existing dataset files on S3,
the 5-6 KiB root-sequence.jsons are pretty negligible when the main
Auspice JSONs are 600-800 KiB. Nextstrain datasets are limited by the
500MB memory cap in Chrome,¹ so we'd be fine adding the
root sequence inline.
This ensures that our uploads will include the root sequence so that
they don't get out-of-sync with the main Auspice JSON.
¹ nextstrain/auspice#1622
Related issue(s)
Follow up to #37
Similar to nextstrain/zika#56
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