Format scripts

[ewels]

The main scripts/nf-core Python script wasn't included in #658 because it doesn't have a .py extension. Updating its code formatting here, plus adding it to the CI.

[codecov]

Codecov Report

Merging #662 into dev will increase coverage by 0.31%.
The diff coverage is 92.59%.

@@            Coverage Diff             @@
##              dev     #662      +/-   ##
==========================================
+ Coverage   76.17%   76.49%   +0.31%     
==========================================
  Files          11       12       +1     
  Lines        2275     2463     +188     
==========================================
+ Hits         1733     1884     +151     
- Misses        542      579      +37     

Impacted Files	Coverage Δ
nf_core/__main__.py	65.42% <92.59%> (ø)
nf_core/sync.py	12.06% <0.00%> (+12.06%)	⬆️

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[ewels]

Ok, Black was still ignoring scripts/nf-core because it didn't have a .py file extension.

I have restructured the repo to use setuptools entry_points instead of script (python-packaging docs). This is better as everything is now in the nf_core Python package. It also means that you can now run tools as a Python package with any Python interpreter you like: python -m nf_core instead of just nf-core if you prefer.

Was a bit more of a major change than I intended, but I think it's a change for the good.

[ewels]

Self-merging again because this is the weekend and I want to continue on this code for the nf-core modules functionality.

Sorry for breaking all of the rules! 🙏