Config namespace warnings

[trym-b]

Hi

When using the latest version (1.5.0) of the nextflow language server in VS Code, and use it on the sample listed here: https://training.nextflow.io/2.2/basic_training/config/#config-scopes

alpha.x  = 1
alpha.y  = 'string value..'

beta {
    p = 2
    q = 'another string ..'
}

I get the following warnings: Unrecognized config option 'alpha.y'nextflow

In the following file I do not get the same warning:

params.x  = 1
params.y  = 'string value..'

params {
    p = 2
    q = 'another string ..'
}

This is kind of confusing, as the first snippet is completely valid, but I get the impression that this means custom namespaces are not recommended. My specific use-case is to setup a namespace that contains a bunch of variables that will be re-used and I do not want to use params for this, as they are not variables given through the CLI or similar.

Let me know if I am completely confused or not.

[bentsherman]

Hi @trym-b , thanks for reporting. I am transferring your issue to the training repo as I think the training material needs to be updated to comply with best practices.

In the strict syntax, custom scopes like these are not allowed and cannot be referenced by other config settings in the way that params can. So you must use params if you want re-usable variables in the config.

In practice, they are only reported as warnings because the language server can't recognize third-party plugins yet. But you will get an error if you try to do something like:

process.cpus = alpha.x // error: `alpha` is not defined

I think this example was carried over from the Nextflow docs, and it is only meant to demonstrate the syntax, not the idea of custom scopes. All examples in the Nextflow docs have since been updated to use real config options

[trym-b]

That is very interesting that custom scopes does not actually work. But I confirmed this with the following command:

nextflow use_custom_config.nf

using these files:

# nextflow.config
test.x  = 1
test.y  = 'string value..'

test {
    p = 2
    q = 'another string ..'
}

and

# use_custom_scope.nf
println "$test.x $test.y"

(the config is implicitly picked up by being in the launch dir)

Renaming test to params solves the issue, just like you said.

Thanks for your help @bentsherman

[bentsherman]

If you want to define params in the config and use them in the script, you should define them first in the script and (optionally) override them in the config:

// use_custom_scope.nf
params.x = null
params.y = null

println "$params.x $params.y"

// nextflow.config
params.x  = 1
params.y  = 'string value..'

This is just a best practice for now but will be required in the future -- the script will only be able to use params declared in the script