I have an issue at the intersection of #CE5LG7WMB, #CGRTMASKY, and Nextflow. I created a new pipeline with

nf-core pipelines create

and seemingly all the requested files have been created. However, it throws an error, saying

RuntimeError: Command 'nextflow config -flat [...]' returned non-zero error code '1':
[red]> ERROR ~ Unable to parse config file: '[...]/nextflow.config'

  Cannot read config file include: <https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config>

curl

on the same URL works as intended. What's wrong?

which version of nf-core and nextflow are you using?

Nextflow 25.10.4, nf-core 3.5.2

can you run

nextflow config -flat

on the created pipeline?

I don't have the broken version anymore, as it got completely corrupted (i.e., no git) and so I recreated it without configs. The command wouldn't work there though, same error.

what do you mean with you created it without configs?

I ran

nf-core pipelines create

again and disabled institutional configs in the creator. It's a bespoke workflow on the template, so it's not required for the basic pipeline.

have you set strict syntax somewhere?

I can't have enabled strict syntax, as this happened during pipeline creation, and I don't think the template enables strict syntax by default (yet)

yes, we usually try to catch these things...

It would be nice to dump a YAML before the creation process starts. Would save some typing if something goes wrong.