Support double nesting in nf-schema or required parameters

[luisas]

Description of feature

I have a complicated structure for my required parameters, and I solved it by defining it this way in my nextflow_schema.json

            "oneOf": [
                {
                    "anyOf": [{ "required": ["seqs", "outdir"] }, { "required": ["pdbs_dir", "outdir"] }]
                },
                { "required": ["input", "outdir"] }
            ],

Yet I get the error:

CRITICAL Critical error: [✗] Pipeline schema does not follow nf-core specs:                                                                                                                                
          Default parameters are invalid: {'templates_suffix': '.pdb', 'calc_sim': True, 'calc_sp': True, 'calc_tc': True, 'calc_gaps': True, 'shiny_app': '${projectDir}/bin/shiny_app',                  
         'custom_config_version': 'master', 'custom_config_base': 'https://raw.githubusercontent.com/nf-core/configs/master', 'publish_dir_mode': 'copy', 'max_multiqc_email_size': '25.MB',               
         'validate_params': True, 'pipelines_testdata_base_path': 'https://raw.githubusercontent.com/nf-core/test-datasets/'} is not valid under any of the given schemas  

@mirpedrol mentioned it is because of the double nesting is not supported yet. Would it be possible to support it? Would be fantastic!

[awgymer]

Is this actually the issue?

Based on your error message the deafult params are:

{
  "templates_suffix": ".pdb",
  "calc_sim": true,
  "calc_sp": true,
  "calc_tc": true,
  "calc_gaps": true,
  "shiny_app": "${projectDir}/bin/shiny_app",
  "custom_config_version": "master",
  "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master",
  "publish_dir_mode": "copy",
  "max_multiqc_email_size": "25.MB",
  "validate_params": true,
  "pipelines_testdata_base_path": "https://raw.githubusercontent.com/nf-core/test-datasets/"
}

Which (correctly) is not considered valid against your schema.

You can test this.

Go to online schema validator
and enter your schema and test it against the above json params:

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "oneOf": [
    {
      "anyOf": [
        {
          "required": [
            "seqs",
            "outdir"
          ]
        },
        {
          "required": [
            "pdbs_dir",
            "outdir"
          ]
        }
      ]
    },
    {
      "required": [
        "input",
        "outdir"
      ]
    }
  ]
}

[mirpedrol]

The required parameters don't have a default, that's why we remove all the required from the schema when we validate the defaults in nf-core.
In this case, because there is nesting, we are not removing one of the required and that's why it fails

[mirpedrol]

Here is the code, for reference

[awgymer]

Ok, perhaps I was misled by the title of the issue. This is not an issue of support in nf-schema but rather support for something that nf-schema allows

[awgymer]

Ok, after a little look and play around with some jsonschema code I think that we can actually do this without needing to modify the input schema at all.

Is anyone able to provide a minimal reproducible example of for the issue so that I can check it? (I guess I need a pipeline, a config, and a schema, but also to know which commands throw this error)

[awgymer]

Ok, had to modify the schema still, but took a guess that this was about multiplesequencealign and added the oneOf to a copy of dev branch with a little fix to tools and...:

❯ nf-core pipelines schema lint


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.2.0.dev0 - https://nf-co.re


INFO     [✓] Default parameters match schema validation                                                                            
INFO     [✓] Pipeline schema looks valid (found 47 params)