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Pin anndataR to v0.1.0 #472

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@lazappi
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@lazappi lazappi commented Jun 23, 2025

We now have a GitHub v0.1.0 release of {anndataR}. It would make sense to pin to this version for consistency. I couldn't find the Docker file where this should be done so currently this just has some minor script changes.

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github-actions bot commented Jun 23, 2025 •
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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fmalmeida commented Jul 29, 2025

Hi @lazappi ,
Thanks for sharing. I believe the Dockerfile had been generated privately before since the tools is not available in conda.
On that note, do you think it would be possible to pack it in conda so module can be easier mantained via the seqera containers?

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grst commented Jul 30, 2025 •
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A bioconductor release is planned, isn't it @lazappi?
I think conda recipes are built for all bioconductor packages, so we'll get it "for free" then.

So for now, I'd be pragmatic and just rebuild the container with the latest version.

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lazappi commented Jul 30, 2025

Yep, we are planning to submit to Bioconductor soon and then it should get automatically added to conda. I don't want to do it manually before then to avoid having two conda packages.

FYI we should have a fairly major 0.2.0 this week or so, so it might be worth waiting for that.

@lazappi
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lazappi commented Aug 1, 2025

There is now a 0.2.0 release on GitHub https://github.com/scverse/anndataR/releases/tag/v0.2.0. Note that we have changed the HDF5 backend so you will need to have {rhdf5} instead of {hdf5r} to read/write H5AD files.

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grst commented Dec 3, 2025 •
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anndataR is now officially part of bioconductor. @lazappi do you know why the corresponding bioconductor-anndatar package does not exist yet on bioconda?

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lazappi commented Dec 4, 2025

Not exactly. I'm guessing the conda packages for the latest release haven't been published yet. I don't know what the process for that is but it's handled centrally somewhere.

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@lazappi @fmalmeida @grst