Give better suggestion when modules.json file is out-of-date.

[mashehu]

Running nf-core modules info never recreates the modules.json. So, if it is out-of-date, the suggested help message is not useful. I think explicitly stating a command is more useful here.

[codecov[bot]]

Codecov Report

Merging #1741 (4d608ae) into dev (9c8614b) will increase coverage by 0.08%. The diff coverage is 95.45%.

@@            Coverage Diff             @@
##              dev    #1741      +/-   ##
==========================================
+ Coverage   69.14%   69.22%   +0.08%     
==========================================
  Files          59       59              
  Lines        7133     7142       +9     
==========================================
+ Hits         4932     4944      +12     
+ Misses       2201     2198       -3     

Impacted Files	Coverage Δ
nf_core/modules/list.py	71.83% <ø> (+0.59%)	:arrow_up:
nf_core/modules/modules_command.py	83.56% <ø> (-0.23%)	:arrow_down:
nf_core/modules/modules_json.py	74.65% <95.00%> (+1.28%)	:arrow_up:
nf_core/lint/__init__.py	74.07% <100.00%> (+0.10%)	:arrow_up:
nf_core/modules/remove.py	82.75% <100.00%> (+0.61%)	:arrow_up:

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[mashehu]

@nf-core-bot fix linting

[ErikDanielsson]

I think that a better solution would be to call the ModulesJson.has_modules_file from all commands that use the modules.json -- there is no need to have the user run another command. We could even call it from the ModulesJson.check_up_to_date that checks whether the modules.json correspond to the modules present in the pipeline