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Cellpose fix - custom model and multiple samples #20

Merged
merged 5 commits into from
Nov 20, 2023
Merged

Cellpose fix - custom model and multiple samples #20

merged 5 commits into from
Nov 20, 2023

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kbestak
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@kbestak kbestak commented Nov 15, 2023

Fixed Cellopose custom model usage when multiple samples are given in samplesheet.
Added clahe_skip_pyramid parameter so that small images can be a processed (necessary for testing).

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! - no tests yet
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • CHANGELOG.md is updated.

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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

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github-actions bot commented Nov 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 07d1b30

+| ✅ 158 tests passed       |+
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-20 13:32:40

@FloWuenne
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All fixes we wanted to do to Cellpose are done in this PR so I will merge!

@FloWuenne FloWuenne merged commit 2da1dd5 into dev Nov 20, 2023
4 of 6 checks passed
@FloWuenne FloWuenne deleted the Cellpose_fix branch November 20, 2023 13:34
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2 participants
@kbestak @FloWuenne