I have been using Nextflow for quite some time now, but today I am stuck with this error and I cannot really figure out why it is happening.

I have this simple process that takes 3 input channel:

process anEasyOne {
    container 'legacy:latest'

    input:
        path "groupA/*"
        path "groupB/*"
        path groups_summary

    output:
        path("groups_metrics.tsv")

    """
    compute_metrics.py --a_group groupA --b_group groupB --stats ${groups_summary}
    """
}

A workflow eventually calls this process:

workflow {
    take: a_files
    take: b_files
    take: summary

    main:
        // other independent steps

        anEasyOne(a_files.collect(), b_files.collect(), summary)

        // ... rest of the workflow

}

This workflow is part of a larger project, and it is called as a sub-workflow, but nothing starts: nextflow throws the title error – No such variable: groups_summary – at the very beginning of the computation, right after parsing all script files but before a single process starts running.

This is an extract of the log:

Jun-25 15:36:26.823 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_ed5649e41a62753a: /home/faabiioo/repos/nw/./modules/groups/main.nf
  Script_72aa75353630da24: /home/faabiioo/repos/nw/./modules/singles/main.nf
...
Jun-25 15:36:26.824 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'groups_summary'
Jun-25 15:36:26.856 [main] DEBUG nextflow.Session - The following nodes are still active:
...
groovy.lang.MissingPropertyException: Unknown variable 'groups_summary'
        at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:67)
...

Here is some runtime information:

Version: 23.10.1 build 5891
Created: 12-01-2024 22:01 UTC (23:01 CEST)
System: Linux 6.5.0-35-generic
Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 19.0.2+7-Ubuntu-0ubuntu322.04
Encoding: UTF-8 (UTF-8)
Process: 153318@faabiioo-vm [127.0.1.1]
CPUs: 16 - Mem: 62.9 GB (52.1 GB) - Swap: 2 GB (2 GB)

I have been searching the documentation, and through github issues, and I am quite sure it must be related to channel semantic, but I can’t really figure out what is the error I am making here.

Any help would be appreciated