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Local module revamp #35

Merged
merged 9 commits into from
Dec 8, 2023
Merged

Local module revamp #35

merged 9 commits into from
Dec 8, 2023

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kbestak
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@kbestak kbestak commented Dec 7, 2023

  • renamed CREATEILASTIKTRAININGSUBSET to CROPHDF5
  • renamed TIFFTRAININGSUBSET to CROPTIFF
  • local modules now use the ghcr.io/schapirolabor/molkart-local:v0.0.1 container
  • CREATE_STACK when clause - also applied the size check logic in molkart.nf
  • Added crop_hdf5.py script instead of scripts in mcmicro-ilastik (to save space)
  • pattern to only return cropped images and overview (not versions or full hdf5 image)
  • clahe does not use aicsimageio anymore
  • create stack outputs a pyramidal tif (Palom)
  • updated mesmer module - accordingly added prefix logic (and for maskfilter)

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
  • 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.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@kbestak kbestak added the enhancement Improvement for existing functionality label Dec 7, 2023
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github-actions bot commented Dec 7, 2023

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 Dec 7, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 346e6b8

+| ✅ 158 tests passed       |+
!| ❗  11 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 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 main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • 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 2023-12-08 09:45:44

FloWuenne
FloWuenne requested changes Dec 8, 2023
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@FloWuenne
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Just one little unfinished sentence and good to merge!

@kbestak @FloWuenne
Update CHANGELOG.md
346e6b8 
Co-authored-by: Florian Wuennemann <[email protected]>
This was referenced Dec 8, 2023
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FloWuenne
FloWuenne approved these changes Dec 8, 2023
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LGTM!

@FloWuenne FloWuenne merged commit 68a2028 into dev Dec 8, 2023
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@FloWuenne FloWuenne deleted the local_module_revamp branch December 8, 2023 10:12
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@FloWuenne FloWuenne FloWuenne approved these changes

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@kbestak @FloWuenne