nf-schema support - Githubissues

nvnieuwk commented 2 months ago

PR features:

[x] Minimal support for nf-schema (includes validation of draft 2020-12, definition notation checks...)
[x] Update template schema
[x] Check the pinning of the nf-schema version
[x] Check for draft 2020-12 usage when nf-schema is used
[x] A linting warning that advises the user to migrate to nf-schema
[x] Check the plugin function imports are using nf-schema when nf-schema is specified in the config
[x] we should add a "nf-validation" field in the templatefeatures.yml allowing one to opt-out of using nf-validation.
support nested parameters (Not doing this since this will no longer be supported in the future)

Features that are nice but not urgent (so probably not for this PR)

[x] Check for the usage of the new config options instead of the parameters

nvnieuwk commented 2 months ago

Wait for https://github.com/nf-core/modules/pull/6217 to be merged before merging this PR

nvnieuwk commented 2 months ago

Wait for nf-core/modules#6217 to be merged before merging this PR

Tests are failing because of this

nvnieuwk commented 2 months ago

Not sure what I can do about the snapshotting test :grin:

mirpedrol commented 2 months ago

Not sure what I can do about the snapshotting test 😁

You can update them by running pytest tests/pipelines/test_create_app.py --snapshot-update, only if the update makes sense 😄 which in this case does, I'm not sure why updating the report is failing, but if it were working you could see a report showing the changes like this:

nvnieuwk commented 2 months ago

Thanks that did it! :partying_face:

nf-core / tools

nf-schema support #3116