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New module: scvitools/solo single-cell doublet detection #6891

Merged
merged 22 commits into from
Nov 5, 2024
Merged

New module: scvitools/solo single-cell doublet detection #6891

merged 22 commits into from
Nov 5, 2024

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LeonHafner
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@LeonHafner LeonHafner commented Oct 29, 2024 •
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PR checklist

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label

@LeonHafner LeonHafner added new module Adding a new module draft labels Oct 29, 2024
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@nf-core-bot fix linting

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Module is producing inconsistent hashes for the output anndata object across two nf-test runs.

nictru
nictru requested changes Oct 30, 2024
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Ideas for removing sources of randomness

modules/nf-core/scvitools/solo/templates/solo.py Show resolved Hide resolved
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nictru commented Oct 30, 2024 •
edited by LeonHafner
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Things left to be done:

  • Remove unnecessary seeds
  • Update scvi-tools version and remove batch stuff

@LeonHafner LeonHafner self-assigned this Oct 31, 2024
@LeonHafner LeonHafner marked this pull request as ready for review October 31, 2024 09:59
@LeonHafner LeonHafner requested a review from nictru October 31, 2024 09:59
@LeonHafner LeonHafner removed the draft label Oct 31, 2024
@LeonHafner LeonHafner linked an issue Nov 1, 2024 that may be closed by this pull request
Create nf-core module for SOLO nf-core/scdownstream#115
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@LeonHafner LeonHafner mentioned this pull request Nov 2, 2024
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@LeonHafner LeonHafner linked an issue Nov 4, 2024 that may be closed by this pull request
SOLO returns doublet instead of singlets nf-core/scdownstream#121
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@nictru nictru added this pull request to the merge queue Nov 5, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks Nov 5, 2024
@nictru nictru added this pull request to the merge queue Nov 5, 2024
Merged via the queue into nf-core:master with commit 6951806 Nov 5, 2024
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@nictru nictru deleted the scvitools_solo branch November 5, 2024 13:21
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@nictru nictru nictru approved these changes

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SOLO returns doublet instead of singlets Create nf-core module for SOLO
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