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Add seurat conversion #125

Merged
merged 8 commits into from Jul 5, 2022
Merged

Add seurat conversion #125

merged 8 commits into from Jul 5, 2022

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fmalmeida
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This PR is related to issue #89

It contains a new module that uses a built-in function from seurat R package to automatically convert .mtx files in .seurat files.

@fmalmeida fmalmeida requested review from grst and apeltzer July 4, 2022 07:33
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github-actions bot commented Jul 4, 2022 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2ccdc11

+| ✅ 148 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-04 13:41:33

@fmalmeida fmalmeida linked an issue Jul 4, 2022 that may be closed by this pull request
Automatic conversion to h5ad/seurat files after alignment. #89
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@fmalmeida fmalmeida marked this pull request as ready for review July 4, 2022 08:48
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grst commented Jul 4, 2022

What's currently there looks good to me!

Should we have also have a version where all samples are merged into a single object including the sample metadata?
This is why I initially thought a conversion from h5ad would be easier.

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fmalmeida commented Jul 4, 2022 •
edited

Indeed it makes sense to have all the data stored in the object. I just added these one here for now as a proof of concept with a working script we already had for that.

An easy choice for having this metadata indeed seems a direct conversion from .h5ad to .rds. With that we can do in a single module for both sample-specific objects and the concatenated one, right?

To add this I would just need to find which package best fits to the pipeline ... On slack you proposed https://github.com/mojaveazure/seurat-disk, right? But this one lacks docker image, while luka proposed https://github.com/cellgeni/sceasy which seems to have a bioconda channel.

So maybe I can try sceasy first.

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grst commented Jul 4, 2022

I have no strong feelings regarding the conversion tool. Let's go for sceasy then!

apeltzer
apeltzer approved these changes Jul 4, 2022
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Brilliant, thank you!

@apeltzer apeltzer merged commit a1c6f12 into nf-core:dev Jul 5, 2022
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@apeltzer apeltzer apeltzer approved these changes

@grst grst Awaiting requested review from grst

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Automatic conversion to h5ad/seurat files after alignment.
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@fmalmeida @grst @apeltzer