Update Dorado version?

[mikemc]

The file configs/containers.config says

    withLabel: dorado {
        container = "ontresearch/dorado:sha3d64678bdcbb70971ee56891c01b9902eab9deea"
        // v0.9.1
    }

suggesting we're currently using Dorado v0.9.1 (from Jan 2025), but the current version is v1.3.0 (Nov 2025).

https://github.com/nanoporetech/dorado/releases

[jeffkaufman]

My memory was the last time we upgraded Dorado we ran into serious regressions, so this is something to be careful with.

[mikemc]

@jeffkaufman can you share any more info about the nature of the regressions? It seems like there has been a lot of development of dorado, and I imagine we'll want to update at some point; perhaps we can develop some tests/benchmarking based on these past issues to evaluate new versions.

[jeffkaufman]

@simonleandergrimm do you recall? My vague memory was that the newer version needed different command line arguments to do what we wanted around demultiplexing.

I don't think this should keep us from upgrading, just that we should be careful to test that the new version does what we want and not just assume it's working correctly (or that we've configured it correctly).

[simonleandergrimm]

My vague memory was that we used "latest", which broke the code in unexpected ways that took a long time to debug.

I'm pro updating, but yes this should go hand in hand with running tests/seeing if the existing code breaks. @mikemc happy to chat in person.