Hello, does someone know why my .nf-core.yml fails linting? https://github.com/qbic-pipelines/rnadeseq/actions/runs/11837108241/job/32983409661?pr=252

CRITICAL Config file '/home/runner/work/rnadeseq/rnadeseq/.nf-core.yml' is      
         invalid                                                                
         lint: Input should be a valid string                                   
         lint: Input should be a valid dictionary                               
         lint: Input should be a valid dictionary                               
         lint: Input should be a valid boolean                                  
Error: Process completed with exit code 1.

could it be the empty lines between the entries in

lint

, e.g. before

files_exist

I already tried removing those (and using nf-core pipelines lint locally), the error persists 😬

nextflow_config:
    - manifest.name
    - manifest.homePage
    - config_defaults:
        - params.custom_config_base
        - params.report_file
        - params.references_file
        - params.css
        - params.logo

The issue is this section. According to the types defined in the pydantic model for the

.nf-core.yml

you can have either a list of strings or a list of dicts of strings. But you can’t mix them. I can’t speak to whether that typing is a mistake, but that’s why this fails

Hello @Arthur, I’m sorry but I don’t understand what this means. How do I have to change this section to fix the error? I believe that the structure of the yml has to be like this for the linter to ignore the respective errors, or can I just modify the indents and it will still work? If so, how?

the only way to fix this in the current version is to set it to:

nextflow_config:
    - manifest.name
    - manifest.homePage
    - config_defaults

but a fix is on the way https://github.com/nf-core/tools/pull/3228

Aha, that worked! Thanks Arthur and Matthias!