nf-core modules list works on pipeline repos as well as module repos #2418
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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
CHANGELOG.md
is updateddocs
is updated