User-defined nested param does not evaluate properly within config file

[jamesbaye]

Bug report

Expected behavior and actual behavior

Evaluating a nested parameter in nextflow.config does not return the user-specified value.

Steps to reproduce the problem

nextflow.config:

params {
    foo = true
    bar = params.foo ? "foo is true" : "foo is false"

    nested.foo = true
    nested.bar = params.nested.foo ? "nested foo is true" : "nested foo is false"
}

main.nf:

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

workflow {
    print "$params.foo $params.bar"
    print "$params.nested.foo $params.nested.bar"
}

Program output

nextflow run main.nf --nested.foo false --foo false

false foo is false
false nested foo is true // expected: "nested foo is false"

Oddly, the return value is as expected if line order is switched in config file:
nextflow.config:

params {
    foo = true
    nested.foo = true

    bar = params.foo ? "foo is true" : "foo is false"
    nested.bar = params.nested.foo ? "nested foo is true" : "nested foo is false"
}

Environment

• Nextflow version: 21.04.1.5556
• Java version: 1.8.0_282
• Operating system: CentOS Linux release 7.9.2009
• Bash version: 4.2.46(2)-release

[abhi18av]

Hi @jamesbaye ,

This is a very interesting observation!

I had the hypothesis that nextflow.config is file always meant to be used to specify the parameters declaratively, rather than a sophisticated programming logic in there.

To test this, modified the script a little bit and added the evaluation part to the main.nf as well, as shown below.

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

workflow {

    print "nested.foo: $params.nested.foo - nested.bar: $params.nested.bar"

    def derived_nested_bar =   params.nested.foo ? "nested.foo is true" : "nested.foo is false"

    print "nested.foo: $params.nested.foo - derived_nested_bar: $derived_nested_bar"
}

The config file used was

params {
    nested.foo = true
    nested.bar = nested.foo ? "nested foo is true" : "nested foo is false"
}

The results for the command invocation were

(base) bash-5.0$ nextflow run main.nf --nested.foo false --foo false

N E X T F L O W  ~  version 21.04.2
Launching `main.nf` [ecstatic_fourier] - revision: 1edf06339b
nested.foo: false - nested.bar: nested foo is true
nested.foo: false - derived_nested_bar: nested.foo is false  // <-- As expected

---

I imagine that the reason this happens is because, the nextflow.config file goes through a parsing process to convert it into Groovy classes (Nextflow is a Groovy DSL) and the config file parser does not cater to sophisticated logic within that file.

That logic works perfectly fine once it is expressed into a xyz.nf` i.e. nextflow file which takes care of those derivations.

Oddly, the return value is as expected if line order is switched in config file:

To me, the aforementioned observation is troubling and unexpected 😶

[abhi18av]

Related #1982

[abhi18av]

A fix has been merged recently for this and would be available in the next edge release i.e. 21.12-edge .