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### Current Behavior
I've noticed that we seem to trigger each build twice at the moment at the end of fetch & ingest:
Not sure why
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### Current Behavior
Previously, the nucleotide sequence per record would be included as `sequence`, since we are pulling the nucleotide sequence as part of the NCBI Virus URL
https://github.com/n…
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## What were you trying to do and how can we improve it?
Shutting down the federal government shutdown to slow the spread of the virus and stopping the virus spread of COVID/Monkeypox and Omicron Va…
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I ran the newest version of Cecret on 185 pairs of Covid reads files, and it ran super-fast! I expected to see snps and trees, but they weren’t produced. Here is the command-line: **nextflow run UPHL…
DrB-S updated
5 months ago
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This function would be a more general version of `discord_edgelist`. It would simplify models with multiple diseases as well as standardize the format of the discordant edgelist. (making it related to…
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### Current Behavior
Because of the behavior described in https://github.com/nextstrain/ingest/issues/18, the ingest pipeline does not include sequences in it's fetch from NCBI Virus. This results in…
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Hhow come the backup RSS fetcher only pulls in ~250k stories each day, while the prod system finds almost a million? I've updated the backup one so it has all the RSS feeds that have:
* active=True
…
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The first step in making this repository useful is to populate it with scripts that are currently manually copied around pathogen repos.
See [shared GDoc](https://docs.google.com/document/d/1ThWh_R…
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Tracking updates of www.redditgifts.com
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- [x] 'suppression by virus of host gene expression' >> host transcription shut-off
& children
- [x] 'suppression by virus of host mRNA processing'
- [x] 'suppression by virus of host transcripti…