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loculus-project / loculus

An open-source software package to power microbial genomic databases
https://loculus.org
GNU Affero General Public License v3.0
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Dummy organism runs pipeline version 2 but ebola and mpox run version 1 #1727

Closed chaoran-chen closed 6 months ago

chaoran-chen commented 6 months ago

Both locally and on main, I am observing that for the dummy organism, there is a processing pipeline running with version 2 but for ebola and mpox, there is only a pipeline with version 1. That means that if we submit dummy data before processing any ebola or mpox data, the dummy data will be processed with a pipeline with version 2. Then, data submitted by the ebola and mpox version 1 pipelines will not be accepted anymore.

We should either disable dummy processing pipeline version 2 or run the ebola and mpox pipelines also with version 2.

corneliusroemer commented 6 months ago

I'm not sure I understand. Pipeline versions should be independent per organism, at least that was my (implicit) understanding all along. Don't we treat organisms very independently? Version changes can be anything from a metadata field change, to a dataset update etc, that can apply just for a single organism.

chaoran-chen commented 6 months ago

As discussed in Slack: currently, the pipeline versions are across organisms. Here's an issue to change that: #1728