Support patch file in nf-core modules lint

[ErikDanielsson]

Continuation from #1708 and #1710. This PR adds support for patch files when linting modules. I have added a new module lint test module_patch that checks if a module's patch file is valid and reversible (i.e. we can construct the original files from it). In the other lint tests, the patch is reversed before performing any checking. However, I'm not sure if this is the optimal approach: would it be better in for example the main_nf test to lint the modified file and only report warnings if the lint fails?

I've waited with adding tests for patches in nf-core lint, since I want to do it in a similar fashion as in #1708 and #1710. This is not possible currently due to #1715.

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 #1716 (913c7cd) into dev (fb57fb9) will decrease coverage by 0.74%.
The diff coverage is 46.96%.

❗ Current head 913c7cd differs from pull request most recent head f63a171. Consider uploading reports for the commit f63a171 to get more accurate results

@@            Coverage Diff             @@
##              dev    #1716      +/-   ##
==========================================
- Coverage   68.99%   68.24%   -0.75%     
==========================================
  Files          58       59       +1     
  Lines        6960     7080     +120     
==========================================
+ Hits         4802     4832      +30     
- Misses       2158     2248      +90     

Impacted Files	Coverage Δ
nf_core/lint/__init__.py	73.85% <0.00%> (ø)
nf_core/modules/lint/module_patch.py	12.98% <12.98%> (ø)
nf_core/modules/lint/module_changes.py	52.38% <40.00%> (-30.96%)	⬇️
nf_core/modules/lint/meta_yml.py	63.82% <64.70%> (+0.67%)	⬆️
nf_core/modules/lint/main_nf.py	64.61% <69.23%> (+0.44%)	⬆️
nf_core/modules/modules_differ.py	86.00% <78.12%> (-0.67%)	⬇️
nf_core/modules/nfcore_module.py	90.90% <81.81%> (-4.93%)	⬇️
nf_core/modules/lint/__init__.py	84.05% <100.00%> (-0.74%)	⬇️
nf_core/modules/patch.py	81.81% <100.00%> (+0.33%)	⬆️
nf_core/modules/update.py	78.45% <100.00%> (-0.60%)	⬇️
... and 2 more

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[mirpedrol]

LGTM thanks! :)

[ErikDanielsson]

Thanks for the review!