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

Merging #2418 (56fa2e9) into dev (6b20a81) will increase coverage by 0.04%.
Report is 20 commits behind head on dev.
The diff coverage is 28.57%.

❗ Current head 56fa2e9 differs from pull request most recent head d17b708. Consider uploading reports for the commit d17b708 to get more accurate results

@@            Coverage Diff             @@
##              dev    #2418      +/-   ##
==========================================
+ Coverage   71.07%   71.11%   +0.04%     
==========================================
  Files          87       87              
  Lines        9431     9427       -4     
==========================================
+ Hits         6703     6704       +1     
+ Misses       2728     2723       -5     

Files Changed	Coverage Δ
nf_core/download.py	59.35% <20.83%> (ø)
nf_core/synced_repo.py	82.58% <50.00%> (+1.47%)	⬆️
nf_core/modules/modules_repo.py	77.61% <100.00%> (+2.24%)	⬆️

[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