Support patch file in nf-core modules update

[ErikDanielsson]

Continuation from #1708 (merge that one first). This PR adds support for automatic application of patches created with nf-core modules patch. The command works by looking for the original lines of the current installation in the new version of the module. If they are found, it replaces them with the modified lines. If there is a conflict between the modifications by the patch file and the update, the new files are installed but the patch file is preserved so the user can apply it manually.

The new feature is tested using a special branch in the nf-core/modules-test repository on GitLab containing only the bismark/align module: patch-tester. The branch contains three commits in total: One containing the original version of the module, one where a change has been made that shouldn't affect the patch file created by the tests and one that should. The commands are tested by creating the patch file on the original version of the module, and then trying to update to the different versions.

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 #1710 (1418ce3) into dev (d070fc6) will increase coverage by 0.33%.
The diff coverage is 77.77%.

❗ Current head 1418ce3 differs from pull request most recent head 46f60d7. Consider uploading reports for the commit 46f60d7 to get more accurate results

@@            Coverage Diff             @@
##              dev    #1710      +/-   ##
==========================================
+ Coverage   68.25%   68.59%   +0.33%     
==========================================
  Files          57       58       +1     
  Lines        6744     6820      +76     
==========================================
+ Hits         4603     4678      +75     
- Misses       2141     2142       +1     

Impacted Files	Coverage Δ
nf_core/utils.py	80.50% <33.33%> (-0.48%)	⬇️
nf_core/__main__.py	52.66% <45.45%> (-0.19%)	⬇️
nf_core/modules/modules_differ.py	84.69% <80.00%> (+12.97%)	⬆️
nf_core/modules/patch.py	81.48% <81.48%> (ø)
nf_core/modules/modules_json.py	64.42% <85.00%> (+1.28%)	⬆️
nf_core/modules/update.py	75.60% <88.88%> (+2.46%)	⬆️
nf_core/modules/__init__.py	100.00% <100.00%> (ø)
nf_core/modules/test_yml_builder.py	48.16% <0.00%> (-0.46%)	⬇️
nf_core/modules/modules_repo.py	82.16% <0.00%> (+0.63%)	⬆️
... and 1 more

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[mirpedrol]

👍

[ErikDanielsson]

Thanks for the review! I need to handle the merge conflict before merging though, its a pretty tricky one