Initial implementation of antsRegistration_affine_SyN.sh

[gdevenyi]

Describe your changes

Implement the CoBrALab variant of antsRegistrationSyN.sh with optimized pyramids.

List test packages used by your module

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
• 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
  • Ensure your variables have good, clear names

[AlexVCaron]

Minimal work is required so the module fits with the nf-core framework. Modules names can only be composed of capital alphanumerical characters and must follow the category/module filenaming convention. So here, it would be (with category) REGISTRATION/COBRALABANTS, using the current file hierarchy.

Once done, most linting and testing should work out the box. But nf-test expects some naming/formatting, that sadly isn't targetted when nf-core conventions are not abided to.

[gdevenyi]

@AlexVCaron I can't sort out how to run the test properly inside the devcontainer, what's the appropriate command?

[AlexVCaron]

I run the test suite for any component from the root of the repo via : nf-test test <path-to-component-base-directory> --update-snapshot --clean-snapshot

In this case, the path is modules/nf-neuro/registration/cobralab_ants

For the lint, it is done via the nf-core command, from the root of the repo again, but without the full path, just the component name : nf-core modules lint registration/cobralab_ants

Tell me of any problems, I can pull your PR and help debug !

[gdevenyi]

Right. OK. It seems like the devcontainer doesn't have the antsRegistration_affine_SyN.sh that I got merged into the main repo...

[AlexVCaron]

I'll get into that this w-e. It should've been included in the build, I'll investigate

[AlexVCaron]

As stated on scilus/containers-scilus#42, scilus/scilus:dev is the container including the dependency for now.