Nextflow StackOverflowError due to undefined workflow metadata

Created on August 24, 2025

2025   ·   nextflow   ·   troubleshoot

I was developing a nextflow workflow and wanted to get the directory where my main.nf is located inside the workflow. I need to run a few Python scripts from the same directory (without hard-coding the absolute path) as part of the workflow.

Cursor suggested a simple variable workflow.scriptDir to retrieve this metadata.

// test_wrong.nf
workflow {
    println "Starting workflow"
    project_dir = workflow.scriptDir
    println "Project directory: ${project_dir}"
}

However, running this simple workflow resulted in a stack overflow error:

ERROR ~ Unexpected error [StackOverflowError]

This is quite strange. I was just trying to get the metadata. It does not even involve any computation.

The .nextflow.log does not help either. It repeated the following error messages hundreds of times before overflowing:

at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:1989)
at groovy.lang.MetaClassImpl.getProperty(MetaClassImpl.java:3898)
at groovy.lang.GroovyObject.getProperty(GroovyObject.java:50)
at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:167)
at nextflow. script.WorkflowMetadata.get(WorkflowMetadata.groovy:357)
at jdk.internal.reflect.GeneratedMethodAccessor15.invoke(Unknown Source)

Fixing…

I just went ahead and asked Cursor to fix it for me. It suggested several solutions (spoiler: none worked), such as:

  • moving the variable to a process/ saving values to a file
  • updating/uninstall/re-install java/openjdk
  • updating/uninstall/re-install nextflow

I tried for a few hours before I found a related discussion in github issue. It turned out that I should use projectDir rather than scriptDir. By default, workflow.projectDir returns the directory of main.nf. So here is a correct version.

// test_correct.nf
workflow {
    println "Starting workflow"
    project_dir = workflow.projectDir
    println "Project directory: ${project_dir}"
}

It is unclear why accessing an invalid variable will invoke a stack overflow. A better (or correct) error message should be Variable not found.

Take-home + TL;DR

Only 4 constants are globally available (retrieved from doc in Aug 2025).

  • baseDir: Path

    Deprecated since version 20.04.0.

    Alias for projectDir.

  • launchDir: Path

    The directory where the workflow was launched.

  • projectDir: Path

    The directory where the main script is located.

  • secrets: Map<String,String>

    Map of pipeline secrets. See Secrets for more information.

More runtime metadata is documented at https://dokk.org/documentation/nextflow/v23.04.4/metadata/

Attempting access to undefined workflow.metadata_variable will give you a stack overflow.

Software versions

# java -version
openjdk version "17.0.15" 2025-04-15
OpenJDK Runtime Environment Homebrew (build 17.0.15+0)
OpenJDK 64-Bit Server VM Homebrew (build 17.0.15+0, mixed mode, sharing)
# nextflow -v
nextflow version 25.04.6.5954