nextflow-io / nextflow

A DSL for data-driven computational pipelines
http://nextflow.io
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null value in publishDir causes Nextflow to hang without error #5041

Closed amrei-bp closed 1 week ago

amrei-bp commented 4 weeks ago

Bug report

(Please follow this template replacing the text between parentheses with the requested information)

Expected behavior and actual behavior

A spelling mistake in the publishDir directive led to Nextflow hanging and reporting no error even though the process showed a completed exit code.

Steps to reproduce the problem

params.outdir = 'output'

workflow {
    DOSOMETHING()
}

process DOSOMETHING {
    publishDir "$param.outdir/something" // <- spelling mistake in variable

    script:
    """
    touch file.ext
    """

    output:
    path "file.ext"
}

Program output

$ nextflow run test.nf 

 N E X T F L O W   ~  version 24.04.2

Launching `test.nf` [magical_brahmagupta] DSL2 - revision: d43e663ce6

executor >  local (1)
[0b/0aebed] DOSOMETHING | 0 of 1

And then stays hung.

Environment

Additional context

(Add any other context about the problem here)

pditommaso commented 1 week ago

Thanks for reporting this issue. This is going to be solved by https://github.com/nextflow-io/nextflow/issues/5041