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added gpu profile for cellpose #91

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added gpu profile for cellpose #91

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kbestak
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@kbestak kbestak commented Oct 30, 2024 •
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TODO: support for Stardist (waiting for cpu stardist merge).
Currently I built a local cellpose container with CUDA 12.2 hosted on kbestak/cellpose:3.0.1_cuda12.2 is there a better way to handle this?
Outputs from GPU version of Cellpose are inconsistent with CPU outputs - by a couple of pixels
Should a Cellpose_GPU module be added with the same functionality so that reproducibility can at least be tested for?

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/molkart branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Oct 30, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 67a5eee

+| ✅ 221 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-02 17:38:29

@nictru
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nictru commented Nov 7, 2024

Hey, could you add the changes I made to nextflow.config in this commit to your implementation?

Basically it sets docker to mount all available GPUs and it removes the --no-mount-tmp --writable-tmpfs, which was a workaround for permission problems when using Singularity/Apptainer

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@kbestak @nictru