Modules refactoring

[KevinMenden]

This PR combines all of the changes that were necessary to adapt the code to the new structure of nf-core/modules and nf-core pipelines.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[codecov]

Codecov Report

Merging #1171 (7c8f113) into dev (004b2dd) will decrease coverage by 0.87%.
The diff coverage is 65.05%.

@@            Coverage Diff             @@
##              dev    #1171      +/-   ##
==========================================
- Coverage   71.56%   70.68%   -0.88%     
==========================================
  Files          29       48      +19     
  Lines        3355     5107    +1752     
==========================================
+ Hits         2401     3610    +1209     
- Misses        954     1497     +543     

Impacted Files	Coverage Δ
nf_core/licences.py	25.00% <0.00%> (-61.74%)	⬇️
nf_core/lint/actions_schema_validation.py	90.62% <ø> (ø)
nf_core/sync.py	51.79% <30.76%> (-0.70%)	⬇️
nf_core/launch.py	64.93% <42.50%> (-2.10%)	⬇️
nf_core/__main__.py	56.91% <43.03%> (-7.28%)	⬇️
nf_core/modules/module_utils.py	44.52% <44.52%> (ø)
nf_core/modules/test_yml_builder.py	45.98% <45.98%> (ø)
nf_core/download.py	54.98% <46.47%> (-9.79%)	⬇️
nf_core/modules/install.py	49.57% <49.57%> (ø)
nf_core/list.py	80.65% <54.16%> (-1.65%)	⬇️
... and 68 more

---

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[KevinMenden]

Okay looks good from my side, just two changes for the code I added

[github-actions]

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install black: pip install black
• Fix formatting errors in your pipeline: black .

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Thanks again for your contribution!

[ErikDanielsson]

Looks good in general to me!

[KevinMenden]

Nice, thanks! Now all we need to is to make black happy and then we can merge this beast 😅