nf-core modules list works on pipeline repos as well as module repos

[adamrtalbot]

Handles case where nf-core modules list would not work on pipeline repos because of missing org_path value in nf-core YAML file. In theory, this should work regardless of the nf-core definitions as long as the structure of the repository looks like nf-core, e.g. ./modules/local/....

This now uses the existing utility function to retrieve the organisation automatically and should provide a prompt if it is missing. I haven't updated the tests but they do not appear to cover this use case so I should.

I did try to harmonise SyncedRepo class to be more consistent everywhere but there are a number of circular dependencies that appear very quickly and this would take longer than I have right now. There are multiple copy-pasted uses of methods in this class so we should resolve this.

Fixes #2417

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

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 71.11%. Comparing base (32bd8c5) to head (56fa2e9).
Report is 1 commits behind head on dev.

❗ Current head 56fa2e9 differs from pull request most recent head fb24d75

Please upload reports for the commit fb24d75 to get more accurate results.

Files	Patch %	Lines
nf_core/synced_repo.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #2418      +/-   ##
==========================================
- Coverage   76.07%   71.11%   -4.97%     
==========================================
  Files          81       87       +6     
  Lines        9155     9427     +272     
==========================================
- Hits         6965     6704     -261     
- Misses       2190     2723     +533     

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[mirpedrol]

LGTM when all tests pass, thanks for the fix!

[mirpedrol]

There are multiple copy-pasted uses of methods in this class so we should resolve this.

I would leave this for a different PR