Hi! I am having an issue with param validation in my own fork of nf-core/stableexpression. When running the pipeline (whatever the parameters), I get a warning like:

WARN: The following invalid input values have been detected:

* --nb_top_gene_candidates: 5000
* --config_profile_description: Minimal test dataset to check pipeline function
* --validate_params: true
* --custom_config_base: <https://raw.githubusercontent.com/nf-core/configs/master>
* --stability_score_weights: 0.8,0.1,0.1,0
* .... any many other params (but not all of them)

The thing is that all of these params are specified in nextflow_schema.json, and that I am using proper type / pattern for all of them. I am using the latest versionof nf-core/tools (3.4.1). Do you know where that could come from? You should be able to reproduce the error by running:

nextflow run OlivierCoen/stableexpression -profile apptainer,test -r dev -latest

Thanks a lot!

I'm not 100% sure, but I think maybe your jsonschema is malformed. I'm on mobile and the GitHub app highlights the final curly bracket in red, which suggests maybe it's unpaired? A quick glance suggests there might be an extra closing brace at the end of your

properties

under

generic_options

. If this is the case though I am surprised that nf-schema does not throw a more serious error. Please check if this is the issue, and whether nf-schema made any noise about it in the

.nextflow.log

. If this is the problem then please open an issue about this on the nf-schema repo as a malformed jsonschema should raise some sort of error

Thank you for the quick answer 🙂 You're right, that was the problem. I did not think to check the validity of the schema file itself since I supposed, as you said, that such errors would result in pipeline failture.

If you could open an issue on nf-schema GitHub that would be great.

Here it is: https://github.com/nextflow-io/nf-schema/issues/187