Update to use tractoflow subworkflow

[AlexVCaron]

Switch the current implementation to use the tractoflow subworkflow from nf-neuro. I had to do some fixes in some modules and subworkflows to make things work. I have PRs incomming to nf-neuro to propagate those fixes.

Tractoflow profiles (ABS, GPU, etc.) not yet implemented.

The current implementation comes with 2 tests profiles :

• test : DWI + rev EPI + T1w
• test_full : DWI + rev DWI + T1w

Currently, you need to have the mni_152_sym_09c template (or the one of your choice) downloaded locally (e.g. in the workdir where you'll run the tests) and supplied using --template_t1. We should think about adding a module to download atlases when they are not supplied directly or unavailable because the pipeline is not run inside of docker.

Here is an example command to run a test :

nextflow run <nf-tractoflow directory> -profile docker,test --outdir <workdir>/results/ --template_t1 <workdir>/mni_152_sym_09c/t1 -resume

I intend to implement more tests, but we should discuss which ones we want so I don't do too much.

[gagnonanthony]

I like it! The main workflow file is super clean. It is a bit hard to review due to the 380 files changed, so I don't have any specific changes, but more questions:

1. I saw that the currently supported input format is the samplesheet? Do we want to start like this first, then move to BIDS or something else?
2. The test cases currently are not using nf-test but are directly calling the pipeline. I know this is how the CI actions are set up by default, but should we switch to nf-test? This could be interesting to perform some assertions after each test runs.

Great job again! 💯