Code maintenance

[fabianegli]

A couple of minor code changes - mostly maintenance but also fixes one function call that had too many arguments.

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 #1747 (cd0e5a4) into dev (ccad6e6) will decrease coverage by 0.03%.
The diff coverage is 70.52%.

@@            Coverage Diff             @@
##              dev    #1747      +/-   ##
==========================================
- Coverage   68.45%   68.41%   -0.04%     
==========================================
  Files          59       59              
  Lines        7136     7121      -15     
==========================================
- Hits         4885     4872      -13     
+ Misses       2251     2249       -2     

Impacted Files	Coverage Δ
nf_core/licences.py	23.94% <0.00%> (ø)
nf_core/lint/__init__.py	73.85% <0.00%> (ø)
nf_core/modules/lint/module_patch.py	10.66% <0.00%> (ø)
nf_core/modules/lint/module_tests.py	70.73% <0.00%> (ø)
nf_core/modules/remove.py	82.14% <ø> (-1.73%)	⬇️
nf_core/refgenie.py	75.67% <0.00%> (ø)
nf_core/__main__.py	52.66% <33.33%> (ø)
nf_core/modules/modules_repo.py	82.38% <50.00%> (ø)
nf_core/modules/modules_json.py	72.05% <60.00%> (ø)
nf_core/utils.py	81.12% <64.28%> (+0.15%)	⬆️
... and 17 more

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[fabianegli]

@mirpedrol Thank you for the review and approving the PR (and the ones just before). 😄