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"Process is already defined" error with nested subworkflows #6533

@sstrong99

Description

@sstrong99

Bug report

Expected behavior and actual behavior

When a subworkflow is used more than once in an workflow, and it is sometimes included from a different subworkflow, it raises the error

A process named '...' is already defined or included in script

Steps to reproduce the problem

decompress this MWE

Run

NXF_SYNTAX_PARSER=v2 nextflow run .

Program output

 N E X T F L O W   ~  version 25.10.0

Launching `./main.nf` [boring_rutherford] DSL2 - revision: bb66e6056d

A process named 'PROCESS' is already defined or included in script: ./mwe/subworkflow.nf

Environment

  • Nextflow version: 25.10.0 with NXF_SYNTAX_PARSER=v2
  • Java version: 21.0.2
  • Operating system: macOS
  • Bash version: GNU bash, version 3.2.57(1)-release (arm64-apple-darwin25)

Additional context

Note that if i move all the subworkflows to be defined in main.nf, instead of in separate files, the workflow runs successfully. Also, the error only occurs with NXF_SYNTAX_PARSER=v2

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