[Module] ihMT module

[karanphil]

Describe your changes

I added a module for ihMT. Could not test it since I am waiting for scilpy 2.0. @Manonedde

Say which test data are used by your module

It uses ihMT.zip.

Checklist before requesting a review

• Create the tool:
  • Edit ./modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./modules/nf-scil/<category>/<tool>/meta.yml
• Generate the tests:
  • Edit ./tests/modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./tests/modules/nf-scil/<category>/<tool>/nextflow.config
  • Add test data locally for tests with the fork repository
  • Generate the test infrastructure and md5sum for all outputs
• Ensure the syntax is correct :
  • Check indentation abides with the rest of the library (don't hesitate to correct others !)
  • Lint everything. Ensure your variables have good names.

[Manonedde]

LGTM!

NB: Are we going to make a module for “classic” MT images? I know there are people at Max who don't use ihMT, but could MT be a “myelin” sub-workflow?

[karanphil]

LGTM!

NB: Are we going to make a module for “classic” MT images? I know there are people at Max who don't use ihMT, but could MT be a “myelin” sub-workflow?

It would be easy to almost copy paste this ihmt module and do a "mt" module. I plan to do it someday.

[AlexVCaron]

Two things, then this should be ready :

• Update your container to 2.0.2
• the comp_maps output in your tests is always empty. Is it normal ?

[karanphil]

Two things, then this should be ready :

• Update your container to 2.0.2
• the comp_maps output in your tests is always empty. Is it normal ?

Good point, there was an option missing in the scil script command line.

[AlexVCaron]

🚀