-stub flag triggers error "Cannot invoke method clone() on null object"

[xuyangyuio]

Bug report

-stub flag breaks workflow with error message "Cannot invoke method clone() on null object"

Expected behavior and actual behavior

• Without -stub flag, pipeline completes successfully.
• With -stub flag, got error "Cannot invoke method clone() on null object"

Steps to reproduce the problem

test.nf:

process mockup {
    output:
    file "*.vcf"

    script:
    """
    touch "real.vcf"
    """
    
    stub:
    """
    touch "stub.vcf"
    """
}

process continue_run {
    input:
    file infile

    """
    echo success
    """
}

workflow {
  mockup | continue_run
}

nextflow run test.nf -stub

Program output

ERROR ~ Error executing process > 'continue_run'

Caused by:
  Cannot invoke method clone() on null object



 -- Check '.nextflow.log' file for details

Environment

• Nextflow version: 24.10.0 (actually since 24.09.1-edge)
• Java version: openjdk version "23" / "21.0.5"
• Operating system: macOS / Linux
• Bash version: zsh 5.9 / bash 5.1.4

Additional context

(Add any other context about the problem here)

[GallVp]

I am experiencing the same issue but without -stub.

[bentsherman]

@jorgee can you look into this one, might be a regression from the recent changes we made