Has anyone seen a linting error like below (link)? Working on the 4.1.0 template merge for nf-core/funcscan. (Please ignore all other CI fails, they are due to database download issues.)

ERROR    Could not parse Nextflow config for
         '/home/runner/work/funcscan/funcscan'. Possibly because of a Nextflow
         version mismatch?
         Command 'nextflow config -o json /home/runner/work/funcscan/funcscan'
         failed with exit code 1
         Downloading plugin nf-schema@2.7.2
         ERROR ~ No such variable: meta
Error: Process completed with exit code 1.

I think I had the same error which led me to this: https://nfcore.slack.com/archives/C04QR0T3G3H/p1788428388351539?thread_ts=1788428388.351539&cid=C04QR0T3G3H

Thanks for the related discussions! Helped me solve it. Only 2 modules had such lists of maps in their

modules.config

, I updated them accordingly.

yep..this is what the bots had suggested me to do..but do you trust these people with updating??

I am having the same issue, and opted for pinning my nextflow version to

"25.10.4"

. That resolves the issue with the publishDirs, but now linting fails because my linting.yml doesn’t match the template. Fixing that with

nf-core pipelines lint --fix

then removes the version pin in linting.yml (as expected). This is a weird catch 22. How did everyone else make this work? I cannot see the magic that breaks the cycle in the funcscan PR by @Jasmin Frangenberg nor the viralmetagenome PR by @Joon Klaps 😮‍💨 Yet you both have passing tests 😅