Process already defined: upgrading to 25.10.0 with strict syntax

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1

i’m working on upgrading a pipeline that ran on nextflow 24.10.3 to 25.10.0 with strict syntax enabled.

I’m getting an error

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

The workflow in question is pretty simple and only includes the process once. e.g.

include { MY_PROCESS } from './my_process'

workflow MY_WORKFLOW {
    take:
    ...

    main:
    MY_PROCESS()
    ch_out_1 = MY_PROCESS.out.out1
    ch_out_2 = MY_PROCESS.out.out2

    emit:
    out1 = ch_out_1
    out2 = ch_out_2

Does something about this syntax need to change for 25.10 and strict syntax?

2

I don’t see any issue with what you’ve written there.

3

huh ok. I have so far been unable to create a MWE. I will keep trying. I was hoping others had seen something similar when migrating

4

I was able to create a MWE. When I do

nextflow run .

with the files below, i get the error “A process named ‘PROCESS’ is already defined or included in script: ./subworkflow.nf”.

Note that if i move all the subworkflows to be defined in main.nf, instead of in separate files, the workflow runs successfully.

main.nf (144 Bytes)

process.nf (77 Bytes)

subworkflow.nf (77 Bytes)

subworkflow1.nf (90 Bytes)

5
6

Thanks Steven for reporting this and the other withName issue. I think they are both bugs. I will try to sort them out this week, and hopefully include fixes in 25.10.1

7

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