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Added multiple sequencing methods #47

Merged
merged 19 commits into from
Jul 19, 2024
Merged

Added multiple sequencing methods #47

merged 19 commits into from
Jul 19, 2024

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RobJY
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@RobJY RobJY commented Jul 9, 2024

PR checklist

  • This comment contains a description of changes (with reason).
    • This PR adds multiple segmentation methods
  • 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/mcmicro branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
    • there are some lint failures, but they look like they're related to template update
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
    • I set the segmentation default to mesmer so it passes
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
    • Have not updated this because I'm not sure if the segmentation input parameter format will change
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@RobJY RobJY requested a review from jmuhlich July 9, 2024 18:59
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github-actions bot commented Jul 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9d187b3

+| ✅ 176 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  25 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • 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: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 README.md: Add bibliography of tools and data used in your pipeline
  • 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 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
  • 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: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • schema_lint - Parameter input not found in schema

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-18 21:44:45

@RobJY
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RobJY commented Jul 9, 2024

Please let me know if you see anything wrong or places it could be improved.
There must be a better way to accumulate the masks from each segmentation method, but I haven't been able to figure anything else out. Any suggestions on how to make this part better? Thanks!

@RobJY
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RobJY commented Jul 9, 2024

Ah, just realized I didn't add everything for the optional cellpose model. Adding that now.
Apologies for jumping the gun.

@RobJY
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RobJY commented Jul 10, 2024

ok, I've got the infrastructure added for using pretrained models with cellpose and added a test for it. I just grabbed that model from their website. Is that an acceptable one to use for our tests?
Either way we'll have one more file that we'll have to add to the test data repo later.

jmuhlich
jmuhlich reviewed Jul 12, 2024
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jmuhlich
jmuhlich reviewed Jul 18, 2024
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@jmuhlich jmuhlich merged commit cc4a219 into nf-core:dev Jul 19, 2024
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@RobJY @jmuhlich