Pydeface module

[loboehme1]

Describe your changes

This PR adds a new PYDEFACE module under modules/nf-neuro/anonymization/pydeface.
The module runs PyDeface on anatomical MRI NIfTI files to remove facial structures for anonymization.
It takes a tuple containing sample metadata and an input NIfTI image, creates a BIDS-like output path using subject and session metadata, and emits the defaced NIfTI image, log files, and software version information.

List test packages used by your module

The module test uses the nf-neuro LOAD_TEST_DATA subworkflow to provide a test T1w NIfTI image.
Test data/package used: T1w.zip

The test checks that:

• The PYDEFACE process completes successfully
• One defaced NIfTI file is produced
• Output logs are created
• The output filename matches the expected *_defaced.nii.gz pattern
• Output files exist and are non-empty

Checklist before requesting a review

• Create the tool:
  • Edit ./modules/nf-neuro/<category>/<tool>/main.nf
  • Edit ./modules/nf-neuro/<category>/<tool>/meta.yml
  • Edit ./modules/nf-neuro/<category>/<tool>/environment.yml --> we use the PyDeface container directly
• Generate the tests:
  • Edit ./modules/nf-neuro/<category>/<tool>/tests/main.nf.test
  • Run the tests to generate the main.nf.test.snap snapshots
• Ensure the syntax is correct :
  • Run prettier and editorconfig-checker to fix common syntax issues
  • Run nf-core modules lint and fix all errors --> there are still a few errors and warnings
  • Ensure your variables have good, clear names

[AlexVCaron]

Excellent work ! My comments and suggestions should get everything inline with our guidelines 🙂 Don't hesitate to get in touch here or via slack if you need my help !