[Project] Make nf-core create more customisable

[ewels]

The nf-core template is central to the community and is increasingly important, both as the community grows (more nf-core pipelines) and as the tooling is used for non nf-core pipelines more and more.

There are a few specific tasks to do here, this issue is to track the overall progress.

Tasks

Beta Give feedback

1. [create] More info / automation about creating a GitHub repository #2166
   command line tools documentation +2
2. [create] Remove --no-git flag #2081
   command line tools +1
3. [create] Option to set branch names #1961
   command line tools +1
4. [create] Improve logic in CLI wizard #2341
   command line tools +1
5. Template: More feature flag granularity #2342
   template +1
6. Template: Opt-in to installation of default modules #2285
   template +1
7. Template: Better handling of params.fasta requirement #2289
   template +1
8. [create] Option to work with other SCM providers (GitLab, BitBucket etc) #2343
   template +1
9. [create] Move command from nf-core create to nf-core pipeline create #2347
   command line tools +1
10. Add template information to .nf-core.yml file #2359
    enhancement infrastructure template +3
    
11. Add option for custom child-template repo #2898
    command line tools +1
12. Pipelines create: fetch list of user repos to push the pipeline #2962
    +0
13. [create]: different pipeline name validation for nf-core and custom pipelines #2963
    enhancement +1
14. [create]: Show org + repo name that will be created #2964
    enhancement +1
15. [create]: Add button to open the created repo #2965
    enhancement +1
16. [create]: Make textual tests pass locally #2975
    enhancement +1
17. Manual include or exclude specific files in template #3088
    +0

[mashehu]

@adamrtalbot created this minimal viable nf-core pipeline, which could be a good target for this rewrite with all flags disabled: https://github.com/adamrtalbot/nf-stem/

[kenibrewer]

Got pointed towards this issue by @edmundmiller, definitely excited about these additional customization features. #1961 in particular has been on my feature wishlist for some time.

@adamrtalbot Just took a look at your nf-stem project. It looks like a great approach! Will probably use your version the next time I do a project that calls for a minimal template.

[adamrtalbot]

Thanks @kenibrewer, your version was a big inspiration.

For what it's worth, I think we can go further now. More streamlined than ever!