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Update README instructions for Nextclade re-runs #479

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Oct 9, 2024
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Update README instructions for Nextclade re-runs #479

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8 changes: 6 additions & 2 deletions README.md
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Expand Up @@ -115,9 +115,13 @@ Enter this into the `slack_member_id` field of your alert configuration.
## Rerunning Nextclade ignoring cache after Nextclade dataset is updated

Clade assignments and other QC metadata output by Nextclade are currently cached in `nextclade.tsv` in the S3 bucket and only incremental additions for the new sequences are performed during the daily ingests.
Whenever the underlying nextclade dataset (reference tree, QC rules) and/or nextclade software are updated, it is necessary to perform a full update of `nextclade.tsv`, rerunning for all of the GISAID and GenBank sequences all over again, to account for changes in the data and Nextclade algorithms.
Whenever the underlying nextclade dataset (reference tree, QC rules) and/or nextclade software are updated,
the automated workflow should automatically ignore the cache and do a full re-run of Nextclade
since https://github.com/nextstrain/ncov-ingest/pull/466 was merged.

In order to tell ingest to not use the cached `nextclade.tsv`/`aligned.fasta` and instead perform a full rerun, you need to add an (empty) touchfile to the s3 bucket (available as `./scripts/developer_scripts/rerun-nextclade.sh`):
However, if something goes wrong, it is possible to manually force a full update of `nextclade.tsv`.
In order to tell ingest to not use the cached `nextclade.tsv`/`aligned.fasta` and instead perform a full rerun,
you need to add an (empty) touchfile to the s3 bucket (available as `./scripts/developer_scripts/rerun-nextclade.sh`):

```bash
aws s3 cp - s3://nextstrain-ncov-private/nextclade.tsv.zst.renew < /dev/null
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