ENH: Switch major subworkflows params to inputs via a map of parameters

[gagnonanthony]

Type of improvement

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• Documentation
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Describe your improvement

The use of params within subworkflow were creating issues when we were trying to bind pipeline level parameters with subworkflow levels parameters. This PR switches all params.* within preproc_t1, preproc_dwi, topup_eddy, and tractoflow to a map of paramters supplied as an input called options.

Describe how to test your improvement

Run the tests

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

[AlexVCaron]

Major discussion point here, I see that we passed over it in recent PRs. What is expected to default to True, and what's not ? Now, with optionality, most preprocessing gets skipped (since null params evaluates to false). We should take a pause and fix that here

[gagnonanthony]

I think, since the optionality will now be documented in the meta.yml as an input, shouldn't it become the responsability of the pipeline dev to properly setup their inputs for the subworkflow (meaning the optionality that comes with it)? @AlexVCaron

I also think setting default can be done two ways:

1. We do not set anything to true (as now), and users set them as they like/want.
2. We set everything to true, and users disable what they don't want.

If we start mixing what is by default true and what's not, it can get more confusing rapidly.

[arnaudbore]

GTG