-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

[phaverty-ginkgo]

Are there specific versions of java and nextflow that resolve this bug? Using openjdk 17.0.14 and nextflow 24.10.4 I still see this error when using -stub. Switching back to nextflow 24.04.4 nextflow runs as expected with the -stub flag.

[jorgee]

@pditommaso we have not backported it to 24.10.X. I have added a tag to remember in the next one. I didn't label it in the original PR. @phaverty-ginkgo, it should be it 24.11.0-edge and 24.12.0-edge