Add more ruff rules (B, PTH, RSE, SIM)

[mashehu]

Additional rules we could add:

• "C4", # flake8-comprehensions - better list/dict/set comprehensions
• "RUF", # Ruff-specific rules - includes RUF103/104 for validating suppressions
• "SIM", # flake8-simplify - simplifies code patterns
• "PIE", # flake8-pie - misc lints for common issues
• "RSE", # flake8-raise - unnecessary parentheses on raised exceptions
• "RET", # flake8-return - unnecessary variable assignments before return
• "ARG", # flake8-unused-arguments - finds unused function arguments
• "BLE", # flake8-blind-except - catches blind except clauses
• "A", # flake8-builtins - catches shadowing of Python builtins
• "TRY", # tryceratops - exception handling best practices

[codecov]

Codecov Report

❌ Patch coverage is 66.76218% with 116 lines in your changes missing coverage. Please review.
✅ Project coverage is 78.45%. Comparing base (ee746b3) to head (a84464a).

Files with missing lines	Patch %	Lines
nf_core/pipelines/schema.py	43.33%	17 Missing ⚠️
nf_core/synced_repo.py	28.57%	10 Missing ⚠️
nf_core/pipelines/list.py	62.50%	9 Missing ⚠️
nf_core/pipelines/create/githubrepo.py	30.00%	7 Missing ⚠️
nf_core/components/update.py	62.50%	6 Missing ⚠️
nf_core/pipelines/refgenie.py	0.00%	6 Missing ⚠️
nf_core/pipelines/rocrate.py	62.50%	6 Missing ⚠️
nf_core/modules/modules_json.py	66.66%	5 Missing ⚠️
nf_core/modules/modules_repo.py	16.66%	5 Missing ⚠️
nf_core/components/remove.py	33.33%	4 Missing ⚠️
... and 24 more

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