Hi! I have just started the hello-nf-core path, participating in the Training week. I have tried launching the nf-core demo pipeline, but the run failed with the following error message:
A workflow named ‘UTILS_NFSCHEMA_PLUGIN’ is already defined or included in script: /workspaces/.nextflow/assets/nf-core/demo/subworkflows/local/utils_nfcore_demo_pipeline/main.nf
I have noticed, that an issue has been created about this bug already, but closed by @ewels 2 weeks ago without a solution. Could you please help?
Did you definitely set export NXF_SYNTAX_PARSER=v1 in your environment, as described in the “Getting Started” part of the docs?
Unfortunately the nf-core/demo pipeline isn’t yet quite compliant with the v2 parser, and throws the error you mention if it is set. We working on getting the v2 parser working for all nf-core pipelines at the moment, but for now you need to use v1.
Note that the v1 parser is default in 25.10, but v2 will be default for 26.04. Because all the other Nextflow Training courses are using v2, we set that environment variable by default in the Codespaces environment, so for the nf-core course you have to unset it again.
I have in fact missed that requirement, but running it solved my issue! Also, thank you Phil, for the update on the GitHub issue too, I (and perhaps other googlers) really appreciate the effort!
No worries - thanks for posting the query! It’s the only way we catch this stuff
Bonus side note, if you upgrade to Nextflow 24.10.4 (released yesterday), the nf-core/demo pipeline now runs properly with both the v1 and v2 syntax parser
NXF_VER=25.10.4 nextflow run nf-core/demo ...
I tried and it worked well, though I got an error with params.input not coming through from -profile test that I don’t really understand but I think that’s a separate issue.
but I think that’s a separate issue.