remove unused templates while building

[tiagofilipe12]

Currently flowcraft build copies all python template scripts (associated to different modules) when building a new pipeline. However in some cases we don't use all those templates because the modules that we have built don't require them. This issue is particularly relevant when we want to make these pipelines available through github, in order to be able to run like nextflow run someuser/mypipeline or to make releases of a given pipeline in github or elsewhere.

Take as an example this pipeline that someone (I am not accusing anyone - @cimendes !!! :stuck_out_tongue_winking_eye:) published: https://github.com/B-UMMI/DEN-IM. When you go to the templates folder there is a lot of python scripts that are not required for the pipeline execution. Of course this doesn't affect the execution of the pipeline but for future code interpretation by other users it would be nice to have a cleaner code in these repos, with less unused code.

One solution, that @ODiogoSilva suggested, would be to avoid build module to place all these template scripts in the resulting templates folder and instead copy only the ones that are required by the generated pipeline.

[cimendes]

Although I'm feeling a little bit accused, I agree that the template folder should be cleaned up. I've kept the DEN-IM rep as private for now due to this very issue. It needs to be cleaned up (and documented).