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I've just been reviewing recent changes in ncov-ingest while investigating #471
I noticed that every rule now has gotten 2 new lines `benchmark: "benchmarks/rulename.txt"`. I'm all for benchmarkin…
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## Context
Our automated workflows use short lived AWS credentials for sessions which are limited by the [max_session_duration](https://github.com/nextstrain/infra/blob/814a7e4cd635b40c12fb0c4e83b168…
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I just noticed that ingest is seemingly stuck for at least 2 hours without doing anything? It hasn't yet started any curation. It's not fetching from Genbank nor from GISAID, yet nothing is happening.…
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Follow up to https://github.com/nextstrain/ncov-ingest/pull/451.
We are using the Snakemake `--stats` flag to get workflow stats for [GISAID](https://github.com/nextstrain/ncov-ingest/blob/f5f238b…
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Options such as [`subsampling..min_date`](https://docs.nextstrain.org/projects/ncov/en/latest/reference/workflow-config-file.html#min-date-2) must contain the option flag to `augur filter`, e.g.
``…
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This text:
> This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions.
is added to any dataset on …
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Noting error in the automated genbank/clade-counts workflow:
- [2024-07-23](https://github.com/nextstrain/forecasts-ncov/actions/runs/10069513692)
- [2024-07-24](https://github.com/nextstrain/foreca…
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`augur merge` should support input `--sequences` and `--output-sequences`.
Features:
- Sequences with same id are coalesced right-to-left, as with metadata rows.
- Duplication handling within F…
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Currently, `parse-genbank-location` strictly follows GenBank's documented pattern for geo_loc_name:
https://github.com/nextstrain/augur/blob/66e903af7eafe07c0418d8cc065a1c754a833caf/augur/curate/pa…
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Originally part of https://github.com/nextstrain/augur/issues/1003, but this is a much bigger task than just porting over an existing script!
We have a great list of [manually curated geolocation r…