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Deepcell - Mesmer segmentation for tissues #3187

Merged
merged 20 commits into from
Mar 31, 2023
Merged

Deepcell - Mesmer segmentation for tissues #3187

merged 20 commits into from
Mar 31, 2023

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migueLib
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@migueLib migueLib commented Mar 28, 2023 •
edited

PR checklist

Closes #3076

  • 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 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
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@migueLib
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migueLib commented Mar 28, 2023 •
edited

We don't have test data on the nf-core/test-datasets so far. Waiting on PR nf-core/test-datasets#827 to merge.

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Test data can be found in:
https://www.synapse.org/#!Synapse:syn51239287

@migueLib migueLib added the new module Adding a new module label Mar 29, 2023
@migueLib migueLib enabled auto-merge March 29, 2023 15:33
@migueLib migueLib disabled auto-merge March 29, 2023 15:56
@migueLib migueLib requested a review from FloWuenne March 30, 2023 09:12
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@nf-core-bot fix linting pretty please

FloWuenne
FloWuenne requested changes Mar 30, 2023
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@nf-core-bot fix linting pretty please 🙏

@FloWuenne @matthdsm
Update tests/modules/nf-core/deepcell/mesmer/main.nf
a323eb8 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
@FloWuenne FloWuenne disabled auto-merge March 31, 2023 09:30
@FloWuenne FloWuenne mentioned this pull request Mar 31, 2023
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@FloWuenne FloWuenne added this pull request to the merge queue Mar 31, 2023
Merged via the queue into nf-core:master with commit c0c79f6 Mar 31, 2023
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@matthdsm matthdsm matthdsm left review comments

@FloWuenne FloWuenne FloWuenne approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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new module: DEEPCELL/MESMER_WHOLE_CELL
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@migueLib @FloWuenne @matthdsm @FriederikeHanssen @nf-core-bot