obtain module suggestions from installed modules

[mirpedrol]

Close #1615

When nf-core modules test is run without specifying a module name, the suggestions from the prompt are obtained from the installed modules (instead of nf-core/modules repository).

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!

[codecov]

Codecov Report

Merging #1624 (0b06097) into dev (ee54b9f) will increase coverage by 0.09%.
The diff coverage is 80.95%.

@@            Coverage Diff             @@
##              dev    #1624      +/-   ##
==========================================
+ Coverage   64.68%   64.78%   +0.09%     
==========================================
  Files          55       55              
  Lines        6338     6353      +15     
==========================================
+ Hits         4100     4116      +16     
+ Misses       2238     2237       -1     

Impacted Files	Coverage Δ
nf_core/utils.py	80.48% <ø> (ø)
nf_core/modules/module_test.py	54.79% <80.95%> (+6.51%)	⬆️
nf_core/modules/modules_command.py	87.80% <0.00%> (+4.87%)	⬆️

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[fabianegli]

Hi @mirpedrol This already looks quite nice, but there are a few things that require some more attention.

Aside from the other comments, there should probably be a test to check if the local modules are collected. Such a test would have caught that all_local_modules was assigned, but not used.

[ErikDanielsson]

Looks good in general, and I've made some comments on things that I think should change.

I don't think we should address this in this PR, but we need to think about if we want the --base-path flag to work when running modules commands on local custom modules repos. This would mean that one could specify in which directory the modules are located. We might be overloading the option a bit too much then, but since we are already doing that with the commands it might make sense.

[ErikDanielsson]

LGTM!

Comments now resolved