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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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feat(ena-submission): How to handle revocation and new versions of sequences already submitted to insdc #2428

Open anna-parker opened 2 months ago

anna-parker commented 2 months ago

Updated October 28th

Currently there is no automated handling of revocation or updates.

The cronjob will send us a list of accessionVersions that we have not submitted to ENA: https://github.com/loculus-project/loculus/blob/main/ena-submission/scripts/get_ena_submission_list.py#L42

The submission pod currently blocks us submitting revisions: https://github.com/loculus-project/loculus/blob/main/ena-submission/src/ena_deposition/trigger_submission_to_ena.py#L27

anna-parker commented 2 months ago

However, as we only submit sequences to ENA after manual approval this isn't very urgent.

anna-parker commented 2 months ago

Tagging @corneliusroemer as this should be the next thing we look at after the initial ENA submission pipeline.