New lint test: params_used

[ewels]

Check if all params returned from nextflow config are mentioned somewhere in main.nf.

Will need updating for DSL2 to run with... all .nf files maybe? Or in certain paths?

Closes #1038

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 #1039 (8b5928d) into dev (dee038f) will increase coverage by 0.09%.
The diff coverage is 93.54%.

@@            Coverage Diff             @@
##              dev    #1039      +/-   ##
==========================================
+ Coverage   69.38%   69.48%   +0.09%     
==========================================
  Files          34       35       +1     
  Lines        4299     4319      +20     
==========================================
+ Hits         2983     3001      +18     
- Misses       1316     1318       +2     

Impacted Files	Coverage Δ
nf_core/lint/merge_markers.py	87.50% <ø> (ø)
nf_core/lint/params_used.py	89.47% <89.47%> (ø)
nf_core/lint/__init__.py	76.79% <100.00%> (+0.09%)	⬆️

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[KevinMenden]

Looks good! 👌

Yes that were my first thoughts when reading this, that for DSL2 we'd have to adapt it. I guess if we have a final structure of DSL2 pipelines that should be easy. When looking for all .nf files in the repo that would include all the modules. For starters we could just omit the modules dir, not so sure about subworkflows 🤔 could imagine people using params in there ... but well let's cross that bridge when we get there

[drpatelh]

Yup. Would have to scrape all .nf files in modules/, subworkflows and workflows/ recursively for DSL2. This is with the assumption that all pipelines adopt this structure too.

[drpatelh]

But I think you will have to 🐻 in mind that you can also have local params in DSL2 that don't necessarily have to be defined in nextflow.config. From what I understand this won't be a problem for the way around that we are trying to do things here.