Add pipeline verification function to nf-core lint

[ErikDanielsson]

The nf-core lint command was complaining about missing the modules.json file, as reported in #1198. This PR adds the ModulesCommand.has_valid_pipeline function that checks whether the pipeline is valid and adds the modules.json file if it is missing.

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 #1208 (f60d25b) into dev (2d32038) will decrease coverage by 0.01%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##              dev    #1208      +/-   ##
==========================================
- Coverage   69.47%   69.45%   -0.02%     
==========================================
  Files          49       49              
  Lines        5415     5419       +4     
==========================================
+ Hits         3762     3764       +2     
- Misses       1653     1655       +2     

Impacted Files	Coverage Δ
nf_core/lint/__init__.py	70.27% <50.00%> (-0.32%)	⬇️

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[drpatelh]

Thanks @ErikDanielsson !

and adds the modules.json file if it is missing.

What if don't want need a modules.json file e.g. in the nf-core/fetchngs pipeline we only have local modules

[ErikDanielsson]

If we only a have local modules the command will create a modules.json file with no entries @drpatelh. In my opinion this is better than not having the file at all, since it indicates that we shouldn't have any remote modules present in the pipeline.

[drpatelh]

Sounds reasonable 👍🏽