Skip to content

Add Vizgenpostprocessing/preparesegmentation module #8575

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged

Conversation

mcmero
Copy link
Contributor

@mcmero mcmero commented May 30, 2025

PR checklist

Closes #8441

  • 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:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

This PR adds the preparesegmentation process for cell segmentation using the vizgen-postprocessing tool for the MERSCOPE spatial omics instrument. The plan would be to add runsegmentationontile​ and compiletilesegmentation​ as subsequent modules to create a segmentation subworkflow for the tool.

The test data is prepared within the test module, using generated dummy data plus an existing segmentation image in nf-core/test-datasets, which needs to be renamed and put in an images directory to work with this module.

I could not find a BioContainer or BioConda package for this tool.

@mcmero mcmero changed the title Vizgenpostprocessing/preparesegmentation Add Vizgenpostprocessing/preparesegmentation module Jun 2, 2025
Copy link
Contributor

@LouisLeNezet LouisLeNezet left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for your contribution.
There is a few modification to make it more nf-core like.

@LouisLeNezet LouisLeNezet added awaiting-changes will be closed after 30 days and removed Ready for Review labels Jun 3, 2025
@mcmero
Copy link
Contributor Author

mcmero commented Jun 4, 2025

Thanks you @LouisLeNezet for the review! I've implemented your suggestions. I am getting CI fails now due to an unrelated module. Do you have any suggestions here?

Copy link
Contributor

@LouisLeNezet LouisLeNezet left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for fixing the modules, this is much better !
Just a few comments before merging.

For the CI fail, something bad migth have happen in another PR.
We will look into it.

mcmero and others added 2 commits June 6, 2025 09:48
Co-authored-by: Louis Le Nézet <[email protected]>
Co-authored-by: Louis Le Nézet <[email protected]>
@LouisLeNezet LouisLeNezet added awaiting-changes will be closed after 30 days and removed awaiting-changes will be closed after 30 days labels Jun 6, 2025
@LouisLeNezet
Copy link
Contributor

Hi @mcmero could you set the prefix as mentioned ?

Copy link
Contributor

@LouisLeNezet LouisLeNezet left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ready to go when the test pass !

@LouisLeNezet
Copy link
Contributor

Could you fix the two alignment ?
This should launch the test and it seems that the github action did something weird.

mcmero and others added 2 commits June 10, 2025 18:04
Co-authored-by: Louis Le Nézet <[email protected]>
Co-authored-by: Louis Le Nézet <[email protected]>
@LouisLeNezet
Copy link
Contributor

@mcmero Could you check that your branch is correctly in sync with the master branch.
It looks like you have a difference but I don't have the rights to update it from my side.

@mcmero mcmero enabled auto-merge June 10, 2025 09:30
@mcmero mcmero added this pull request to the merge queue Jun 10, 2025
Merged via the queue into nf-core:master with commit e08e94b Jun 10, 2025
21 checks passed
@mcmero mcmero deleted the vizgenpostprocessing/preparesegmentation branch June 10, 2025 09:34
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
awaiting-changes will be closed after 30 days
Projects
None yet
Development

Successfully merging this pull request may close these issues.

new module: vizgenpostprocessing/preparesegmentation​
2 participants