[ENH] Update topup_eddy subworkflows and eddy module

[AlexVCaron]

Continuation of #26

Type of improvement

• Documentation
• Development tools (e.g. linter, formatter, etc.)
• Development container
• Global update (please specify)
• Other (please specify)

Describe your improvement

subworkflow/topup_eddy:

copy alex's changes for tractoflow

module/preproc/eddy:

• change bval output name: had problem further in the flow caused by lack ox fil extension

Checklist before requesting a review

• Ensure the syntax is correct (EditorConfig and Prettier must pass)
• Run the test suites if your changes affect any module
• Regenerate the Poetry lock file if you have updated the dependencies
• Ensure the documentation is up-to-date

[arnaudbore]

Great job !

[gagnonanthony]

Great job! The comments you added make following the channels straightforward! 💯