Schema has allOf, but no definitions

[chriswyatt1]

Hi,

I am probably doing something really dumb, but I cannot get nf-core schema build to work.

I have an existing repo (https://github.com/Eco-Flow/synteny), that I migrated to the new json style, but it says:

ERROR    [✗] Pipeline schema does not follow nf-core specs:                                                                  
          Schema has allOf, but no definitions                                                                               
ERROR    Existing pipeline schema found, but it is invalid: nextflow_schema.json                                             
INFO     Please fix or delete this file, then try again. 

I then played around with my json file to make it as minimal as possible, but always get this error.

I then tried the example json: https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_examples/ to see if this makes the same error, and for me it does.

I use this in my main.nf: include { validateParameters; paramsHelp; paramsSummaryLog } from 'plugin/nf-schema' Plus:

plugins {
  id 'nf-co2footprint@1.0.0-beta'
  id 'nf-schema@2.0.0'
  id 'nf-amazon@2.1.4'
}

and I am using nf-core tools version 2.13.1. nextflow 24.03.0-edge.5908. I have deleted my nf-schema cache

If anyone can see what I am missing, I would be grateful :)

[pcrxn]

I'm obtaining the same error after migrating an existing workflow to the new style (nextflow_schema.json attached) with nf-core=2.13.1.

[chriswyatt1]

From Júlia Mir : nf-core schema build is not yet updated to use the new JSON draft, the one used by nf-schema, so the migration has to be done manually You can see the docs on how to migrate here nextflow-io.github.ionextflow-io.github.io Migration guide - nf-schema