handle errors when updating module version

[mirpedrol]

Handle errors when trying to update a module version.
Needed for #1745

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 #1671 (dee98e6) into dev (b7f44d3) will decrease coverage by 0.08%.
The diff coverage is 5.26%.

@@            Coverage Diff             @@
##              dev    #1671      +/-   ##
==========================================
- Coverage   69.07%   68.99%   -0.09%     
==========================================
  Files          58       58              
  Lines        6950     6960      +10     
==========================================
+ Hits         4801     4802       +1     
- Misses       2149     2158       +9     

Impacted Files	Coverage Δ
nf_core/modules/lint/main_nf.py	64.17% <5.26%> (-2.23%)	⬇️

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[ErikDanielsson]

Looks good! Just have look at my comment for a minor suggestion (:

[mirpedrol]

I am going to merge this, it finally handles the annoying error with sqlite :) It's something related to a timeout, it's not failing locally.
Some things have changed since the review, if you want to have a final look @ErikDanielsson

[ErikDanielsson]

Code still looks good to me! But you should update the changelog :)

[mirpedrol]

thanks!