Currently, nf-core pipelines have a lot of boilerplate code in the main main.nf script. It would be nice to move this out into a separate file to make the pipeline code easier to read.

This is intended for DSL1 pipelines, but the move will also be useful for DSL2 when we will also want to import this code and call it from functions in the same way.

@pditommaso made a start on this way back in 2018, with a draft PR on the methylseq pipeline: nf-core/methylseq#47

@phue followed up with a draft PR on the hlatyping pipeline nf-core/hlatyping#61 (also included stuff for the now depreciated parameters.settings.json file)

Needs reassessing with the latest version of the pipeline and testing.