pop transformation pipeline

[claude-marie]

No description provided.

[EstebanMontandon]

Hey @claude-marie, could you take a look at the changes in my last commit? I think this is an example of how we should aim to organize code across our pipelines moving forward. Let me know what you think!

Please notice that I have separated the functions in the R file in two groups:
group 1 what should potentially be moved to SNT utils, and
group 2 (after the tag) for functions specific for the pipeline.

The notebook remains step by step in terms of the computation, for this pipeline I don't expect many people will try to modify the code , but if it happens , it will still be more or less understandable of what is going on.

[EstebanMontandon]

let's try to apply a standard