Hi there, I’m unable to resolve some failing linting tests with the new template: What I used to have in my `.nf-core.yml`file for skipping certain tests:

...
  nextflow_config:
    - config_defaults:
        - params.multiqc_comment_headers
        - params.custom_table_headers

Which now results in a invalid config file.

CRITICAL Config file '.nf-core.yml' is invalid

If I change it to :

...
  nextflow_config:
    - params.multiqc_comment_headers
    - params.custom_table_headers

the

.nf-core.yml

can be read but I think those params are being skipped.

nextflow_config: Config default value incorrect: params.multiqc_comment_headers is set as ${projectDir}/assets/mqc_comment in nextflow_schema.json but is /workspace/viralgenie/assets/mqc_comment in nextflow.config.
nextflow_config: Config default value incorrect: params.custom_table_headers is set as ${projectDir}/assets/custom_table_headers.yml in nextflow_schema.json but is /workspace/viralgenie/assets/custom_table_headers.yml in nextflow.config.

The docs (bottom of page) still mention that the first is valid syntax so are they just outdated?

can you please post the complete

.nf-core.yml

here?

and the one with

- config_defaults:

?

okay, the problem is we assumed lint.nextflow_config to either be a list of strings or a list of dictionaries, not a mixture of both... does this work?

nextflow_config:
    - manifest:
        - name
        - homePage
    - config_defaults:
        - params.annotation_db
        - params.multiqc_comment_headers
        - params.custom_table_headers

Thx! I’ll check in a bit and keep you posted

thanks for testing