`nextflow inspect` no longer respects container overrides from config for `withName`

Bug report

In previous versions of nextflow inspect container overrides set using any withName selectors were respected and reported correctly. Since (at least) 25.04 this is broken and overrides only work from withName that uses only the process name (e.g. not alias, fully qualified name, partial qualified process name etc).

Expected behavior and actual behavior

For the following workflow main.nf please see the working/non-working examples.

process A_A { 

    script:
    """
    echo test
    """
}

process A_B { 

    script:
    """
    echo test
    """
}

workflow PARENT {
    A_A()
    A_B()
}

workflow {
    PARENT()
}

Working in both

Process name only

nextflow.config

process {

    withName: A_A {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
        {
            "name": "A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

Quoted process name only

nextflow.config

process {

    withName: "A_A" {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
        {
            "name": "A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

Partial process name

nextflow.config

process {

    withName: "A_.*" {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

nextflow inspect main.nf
{
    "processes": [
        {
            "name": "PARENT:A_B",
            "container": "docker.io/google/deepvariant:1.8.0"
        },
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
        {
            "name": "A_B",
            "container": "docker.io/google/deepvariant:1.8.0"
        },
        {
            "name": "A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

Working only in 24.10.5

Fully qualified process name

nextflow.config

process {

    withName: "PARENT:A_A" {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
    ]
}

Partial qualified process name

nextflow.config

process {

    withName: ".*RENT:A_A" {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
    ]
}

ALIASING

For the following tests module definitions were moved to module.nf and top-level main.nf is now

include { A_A; A_A as A_B } from './module.nf'

workflow PARENT {
    A_A()
    A_B()
}

workflow {
    PARENT()
}

Alias by base name

nextflow.config

process {

    withName: A_A {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_B",
            "container": "docker.io/google/deepvariant:1.8.0"
        },
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
        {
            "name": "A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

Alias by alias

nextflow.config

process {

    withName: "A_B" {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_B",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
        
    ]
}

Alias by alias and base name

nextflow.config

process {

    withName: "A_B" {
        container = "docker.io/google/deepvariant:1.9.0"
    }


    withName: "A_A" {
        container = "docker.io/google/deepvariant:1.8.0"
    }

}

24.10.5

{
    "processes": [
        {
            "name": "PARENT:A_B",
            "container": "docker.io/google/deepvariant:1.9.0"
        },
        {
            "name": "PARENT:A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

25.04.3

{
    "processes": [
        {
            "name": "A_A",
            "container": "docker.io/google/deepvariant:1.8.0"
        }
    ]
}

I haven't tested overrides by e.g. withLabel but as you can see it appears that since at least 25.04.3 the nextflow inspect command reports only "base modules" and not the fully qualified names/paths as in 24.10.5 and this appears to affect the correctness of the reporting.

Environment

• Nextflow version: 25.04.3
• Java version: openjdk version "21.0.7" 2025-04-15 LTS
• Operating system: macOS

Reproduce the regression with nextflow inspect using the main.nf, nextflow.config, and module.nf examples in the report, comparing qualified names, partial selectors, and aliases. Trace how inspect resolves process configuration and verify that its output reports the configured container for the fully qualified and aliased processes as in 24.10.5.