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JosuaCarl opened this issue Mar 13, 2025 · 0 comments
Open

Import error upon local execution #31

JosuaCarl opened this issue Mar 13, 2025 · 0 comments
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@JosuaCarl
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Description of the bug

When trying to execute the workflow in local / dev mode (i.e. with /path/to/nextflow/launch.sh run /path/to/demo/main.nf) the script fails with:

A workflow named 'UTILS_NFSCHEMA_PLUGIN' is already defined or included in script: /path/to/demo/subworkflows/local/utils_nfcore_demo_pipeline/main.nf

 -- Check script '/path/to/demo/subworkflows/local/utils_nfcore_demo_pipeline/main.nf' at line: 11 or see '.nextflow.log' file for more details

I found that the cause of this are the input statements

include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_demo_pipeline'

and
include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin'
include { paramsSummaryMap } from 'plugin/nf-schema'
include { samplesheetToList } from 'plugin/nf-schema'
include { completionEmail } from '../../nf-core/utils_nfcore_pipeline'
include { completionSummary } from '../../nf-core/utils_nfcore_pipeline'
include { imNotification } from '../../nf-core/utils_nfcore_pipeline'
include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline'
include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'

If I remove one of them, the error is gone. But so are the needed methods (of course).

Command used and terminal output

export NXF_PLUGINS_DEV=/Users/josuacarl/Codespace/test/nf-schema/plugins
path/to/nextflow/launch.sh run /path/to/demo/main.nf

Relevant files

.nextflow.log

System information

  • Nextflow version: Current Github main repo
    •   N E X T F L O W
        version 25.01.0-edge build 5931
        created 12-02-2025 10:55 UTC (11:55 CEST)
        cite doi:10.1038/nbt.3820
        http://nextflow.io
      
  • Executor: local
  • OS: MacOS 15.3.1 (Intel Chipset)
  • Version of nf-core/demo: Current Github main branch (1.0.1-edge)
@JosuaCarl JosuaCarl added the bug Something isn't working label Mar 13, 2025
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