Refactor passing of command line arguments to nf-core commands

[ErikDanielsson]

Updated passing of arguments to nf-core commands and subcommands:

• Pipeline directory is now passed with --dir <pipeline directory> with . as default, for all nf-core commands that previously had it as an argument. Resolves Updating handling of <pipeline directory> in nf-core #1140
• Pipeline directory for nf-core modules list is now passed with --installed <pipeline directory>. Partially resolves nf-core modules list behaviour #1139
• --tool <tool name> for nf-core modules subcommand are now replaced by optional argument <tool>. For example: nf-core modules install fastqc.
• Updated docs text, but not the console logs.

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 #1145 (3d8b6af) into dev (9c83171) will decrease coverage by 0.42%.
The diff coverage is 39.17%.

@@            Coverage Diff             @@
##              dev    #1145      +/-   ##
==========================================
- Coverage   69.72%   69.29%   -0.43%     
==========================================
  Files          50       50              
  Lines        5179     5224      +45     
==========================================
+ Hits         3611     3620       +9     
- Misses       1568     1604      +36     

Impacted Files	Coverage Δ
nf_core/bump_version.py	91.52% <0.00%> (+3.00%)	⬆️
nf_core/modules/module_utils.py	41.02% <0.00%> (ø)
nf_core/__main__.py	56.79% <34.66%> (-5.23%)	⬇️
nf_core/lint/__init__.py	75.10% <50.00%> (-0.53%)	⬇️
nf_core/schema.py	84.97% <50.00%> (-0.39%)	⬇️
nf_core/modules/modules_command.py	72.22% <66.66%> (-1.12%)	⬇️
nf_core/utils.py	83.64% <80.00%> (-0.05%)	⬇️
nf_core/modules/bump_versions.py	79.51% <0.00%> (+0.12%)	⬆️

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[KevinMenden]

Looks good, thanks! 👍 ✅

[ErikDanielsson]

Thanks for the review @KevinMenden!

[KevinMenden]

Looks good!

[ErikDanielsson]

Thanks again @KevinMenden!