Add ruff - Replace Black, isort and pyupgrade

[mirpedrol]

Replace PR #2174
Close #2533

Implement Ruff linter. In replacement of Black, isort and pyupgrade. It also includes Flake8.

[codecov]

Codecov Report

Attention: 58 lines in your changes are missing coverage. Please review.

Comparison is base (7831f7a) 75.19% compared to head (eb4b775) 75.00%.
Report is 1 commits behind head on dev.

Files	Patch %	Lines
nf_core/sync.py	50.00%	11 Missing ⚠️
nf_core/download.py	50.00%	9 Missing ⚠️
nf_core/__main__.py	0.00%	8 Missing ⚠️
nf_core/modules/bump_versions.py	33.33%	8 Missing ⚠️
nf_core/modules/lint/main_nf.py	87.75%	6 Missing ⚠️
nf_core/modules/lint/__init__.py	33.33%	2 Missing ⚠️
nf_core/subworkflows/lint/__init__.py	33.33%	2 Missing ⚠️
nf_core/components/info.py	50.00%	1 Missing ⚠️
nf_core/components/lint/__init__.py	50.00%	1 Missing ⚠️
nf_core/launch.py	66.66%	1 Missing ⚠️
... and 9 more

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2620      +/-   ##
==========================================
- Coverage   75.19%   75.00%   -0.19%     
==========================================
  Files          85       85              
  Lines        9384     9363      -21     
==========================================
- Hits         7056     7023      -33     
- Misses       2328     2340      +12     

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