Template: Opt-in to installation of default modules

[buehlere]

Description of feature

Would it be possible to have nf-core create create a more generic pipeline template?

In @anoronh4, @huyu335 and I's use case, we are interested in having all of our institutional pipelines pull from our internal fork of nf-core/modules, and would like our teams to be able to initialize their pipelines with a more generic template that doesn't have modules pre-loaded from nf-core/modules. We are fine with most other aspects of the current template, but removing the pre-loaded modules creates a manual step in pipeline initialization that we'd like to avoid.

From conversation in the nf-core slack, it sounds like there also may be interest in this feature from those who are working on non-bioinformatic pipelines, and that the feature would be similar to the --empty-template option for modules. Please see here for the full conversation.

Let me know if I can answer any questions / how might be best to approach this feature!

[mirpedrol]

Done in the dev branch, will be available with version 3.0.0