Rich click

[ewels]

🆕 CLI help command groups 🤩

Sorting of commands but also breaking up into multiple panels with their own headers:

[ewels]

Need to do a release of rich-click for this to work for everyone else, but shouldn't hurt to merge in ahead of that I think. It should start working once the new release is out.

[codecov]

Codecov Report

Merging #1411 (46a8fe4) into dev (84b5485) will increase coverage by 0.10%.
The diff coverage is 97.56%.

@@            Coverage Diff             @@
##              dev    #1411      +/-   ##
==========================================
+ Coverage   66.77%   66.87%   +0.10%     
==========================================
  Files          50       50              
  Lines        5713     5688      -25     
==========================================
- Hits         3815     3804      -11     
+ Misses       1898     1884      -14     

Impacted Files	Coverage Δ
nf_core/__main__.py	52.60% <97.56%> (-2.90%)	⬇️
nf_core/modules/lint/main_nf.py	80.11% <0.00%> (-1.76%)	⬇️
nf_core/modules/create.py	80.10% <0.00%> (+1.02%)	⬆️
nf_core/utils.py	84.50% <0.00%> (+3.75%)	⬆️

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[mashehu]

Should we mention that one has to be called inside a pipeline repo and one inside the modules repo or will that be too much text?

[ewels]

No such thing as too much text now! Instead of being truncated the plug-in will mean that the text just wraps onto a second line if it's long.

We might want to keep it shortish anyway though, still looks better if they're on one line I think.

[ewels]

Updated to use new rich-click usage (no monkey patching, just import rich-click as click).

Needs new release from rich-click to work, but then should be good to merge.

[ewels]

Version 1.0.0 now released, should be good to go here.

[drpatelh]

🚀

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