Remove nf-core modules check

[ewels]

• Remove "check" command
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615806091239300
• Make it more obvious that commands are not yet implemented in help
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615805322230000
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615805565234000
• Module should not be "install" or "remove" if pipeline directory is invalid
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615804113221800
    https://nfcore.slack.com/archives/CE5LG7WMB/p1615804546224400
• Remove "def options" from the modules template
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615803595218500
• Rename "modules/.github/filters.yml" -> "tests/pytest_include.yml"
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615807094244800
• List modules installed in pipeline as well as on nf-core/modules
  • https://nfcore.slack.com/archives/CE5LG7WMB/p1615803595218500

[codecov]

Codecov Report

Merging #878 (494477f) into dev (bedbe53) will decrease coverage by 0.04%.
The diff coverage is 61.46%.

@@            Coverage Diff             @@
##              dev     #878      +/-   ##
==========================================
- Coverage   71.13%   71.08%   -0.05%     
==========================================
  Files          33       33              
  Lines        3596     3604       +8     
==========================================
+ Hits         2558     2562       +4     
- Misses       1038     1042       +4     

Impacted Files	Coverage Δ
nf_core/list.py	82.23% <ø> (-0.08%)	⬇️
nf_core/modules/test_yml_builder.py	16.98% <0.00%> (-0.11%)	⬇️
nf_core/__main__.py	61.53% <39.28%> (-1.09%)	⬇️
nf_core/modules/create.py	63.75% <73.33%> (+1.75%)	⬆️
nf_core/modules/pipeline_modules.py	86.15% <74.19%> (-2.55%)	⬇️

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[drpatelh]

Do we remove the update command too?

[ewels]

Made an awesome fuzzy-finder interface when installing modules which I kind of love:

[ewels]

Do we remove the update command too?

Yup, it's gone from the command line interface. I commented it out and left the stub as we do intend to put that in at a later date (I completely deleted check as that's part of lint).

[drpatelh]

As mentioned on Slack we need to change where these modules are installed locally:

tools/nf_core/modules/create.py

Line 51 in d0b7daf

'directory/modules/local/process' dir called <tool_subtool.nf>

Need to change this install path to directory/modules/local/ i.e. without the process - based on recent module restructuring in #viralrecon

[ewels]

Dropped process dir in 336de7d 👍🏻

[drpatelh]

Pleasure as always Sir! 💥