Add --base-path option to modules commands (and refactor modules.json code)

[ErikDanielsson]

Added --base-path option to the modules commands to allow custom module directory in a remote repo. This required me to refactor the code for how the modules.json file is handled. It is moved to its own file now: modules_json.py and accessed through a ModuleJson object.

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 #1655 (f8bec09) into dev (9bd0355) will increase coverage by 0.00%.
The diff coverage is 43.97%.

@@           Coverage Diff           @@
##              dev    #1655   +/-   ##
=======================================
  Coverage   64.68%   64.68%           
=======================================
  Files          54       55    +1     
  Lines        6281     6338   +57     
=======================================
+ Hits         4063     4100   +37     
- Misses       2218     2238   +20     

Impacted Files	Coverage Δ
nf_core/modules/module_utils.py	53.53% <ø> (+19.12%)	⬆️
nf_core/modules/update.py	7.63% <10.00%> (-0.19%)	⬇️
nf_core/modules/modules_json.py	30.74% <30.74%> (ø)
nf_core/__main__.py	52.13% <75.00%> (+0.09%)	⬆️
nf_core/modules/lint/module_version.py	85.18% <76.92%> (-0.53%)	⬇️
nf_core/modules/modules_command.py	82.92% <80.00%> (+30.12%)	⬆️
nf_core/modules/remove.py	80.55% <87.50%> (+4.55%)	⬆️
nf_core/modules/modules_repo.py	76.97% <90.00%> (+1.64%)	⬆️
nf_core/modules/install.py	69.23% <93.75%> (+3.01%)	⬆️
nf_core/lint/modules_json.py	80.76% <100.00%> (+2.50%)	⬆️
... and 4 more

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[mirpedrol]

Looks good! I also tested the functionality and it works fine :)

[ErikDanielsson]

Thanks for the review! I'll merge it then.