Add consistency checks between installed modules and modules.json

[ErikDanielsson]

Added consistency checks between modules present in pipeline and modules.json:

• If a module is missing from the directory but is present in the modules.json file we try to reinstall it at the given commit SHA
• If the install fails, we remove the entry in modules.json
• If a module is present in the directory, but missing from modules.json we try figure out the correct one using the file contents. If that fails, we continue but warn the user.

These checks are run when either nf-core modules install or nf-core modules list local are run. Should resolve #1199.

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 #1200 (6edc0fe) into dev (5b6927a) will decrease coverage by 0.62%.
The diff coverage is 33.01%.

@@            Coverage Diff             @@
##              dev    #1200      +/-   ##
==========================================
- Coverage   70.12%   69.49%   -0.63%     
==========================================
  Files          49       49              
  Lines        5312     5403      +91     
==========================================
+ Hits         3725     3755      +30     
- Misses       1587     1648      +61     

Impacted Files	Coverage Δ
nf_core/modules/module_utils.py	45.56% <11.11%> (-1.36%)	⬇️
nf_core/modules/modules_command.py	55.38% <24.65%> (-18.39%)	⬇️
nf_core/modules/install.py	39.53% <100.00%> (+0.71%)	⬆️
nf_core/modules/list.py	69.33% <100.00%> (+0.84%)	⬆️
nf_core/modules/modules_repo.py	65.43% <100.00%> (ø)
nf_core/utils.py	84.13% <100.00%> (+0.28%)	⬆️

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[drpatelh]

LGTM! It's going to be tricky reviewing these PRs having not touched the code base for a while and with everything else I am trying to do at the mo but happy to get this in so it can be tested properly :)

Thanks @ErikDanielsson

[ErikDanielsson]

Thanks for the review @drpatelh!