Remove unused imports

[fabianegli]

Mostly removal of unused imports, with two minor off-topic additions: 1. cleanup of imports in refgenie and 2. replacement of deprecated calls to log.warn.

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 #1706 (eb4e378) into dev (ca4bd32) will increase coverage by 0.22%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##              dev    #1706      +/-   ##
==========================================
+ Coverage   67.98%   68.21%   +0.22%     
==========================================
  Files          56       57       +1     
  Lines        6694     6736      +42     
==========================================
+ Hits         4551     4595      +44     
+ Misses       2143     2141       -2     

Impacted Files	Coverage Δ
nf_core/__main__.py	52.84% <ø> (-0.22%)	⬇️
nf_core/bump_version.py	89.65% <ø> (-0.18%)	⬇️
nf_core/launch.py	63.84% <ø> (-0.10%)	⬇️
nf_core/licences.py	23.94% <ø> (-1.06%)	⬇️
nf_core/lint/actions_schema_validation.py	90.32% <ø> (-0.31%)	⬇️
nf_core/lint/modules_json.py	80.00% <ø> (-0.77%)	⬇️
nf_core/lint/schema_description.py	67.85% <ø> (-1.11%)	⬇️
nf_core/lint/schema_lint.py	75.86% <ø> (-0.81%)	⬇️
nf_core/modules/bump_versions.py	64.40% <ø> (-0.20%)	⬇️
nf_core/modules/lint/main_nf.py	66.39% <ø> (-0.14%)	⬇️
... and 11 more

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[ErikDanielsson]

LGTM!