Hi, I am quite new to nextflow and am trying to run the cutandrun worklow through UPPMAX. I can load the pipeline and manages to run this test sucessfully nextflow run nf-core/cutandrun -profile test However, whenever I run the following code through uppmax I encounter this error. nextflow run nf-core/cutandrun \ -profile uppmax,test \ --input 250717_sample_sheet_cutandrun.csv \ --outdir ./results \ --project uppmax xxxxx WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config ERROR ~ No such file or directory: Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/master/conf/conf/test.config Happy for any suggestions, thanks 🙂

looks like your

custom_config_base

parameter is set wrong somewhere, producing

/conf/conf/

instead of

/conf

. can you check that?

I am trying to load the shared nf-core/config files on uppmax and have therefor not specified these anywhere. Can I check what this is set to?

ah, i think the problem is that you try to run the test profile and then add an additional input. try to just use

-profile uppmax \

That should still work (or, the input might of course break the pipeline but config should be fine). In fact, site configs shouldn't be called unless explicitly listed, which shouldn't be the case for test. Do you see the same for other pipelines (e.g. sarek or rnaseq)?

Thanks. I tried to run without the test profile and get a similar error: WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config ERROR ~ Plugins definition is only allowed in config top-most scope

Thanks. Are you using nextflow from the module system or one you installed yourself?

I am using the one from the module system.

Hrrm, what system is this on?

I am working on the Rackham cluster on Uppmax!

https://github.com/nf-core/configs/pull/939 Can be tested by adding

--custom_config_base <https://raw.githubusercontent.com/pontus/nf-core-configs/refs/heads/rackham_bugfix_20250725/>

to the command. I hope it works with that.

It seems to be working now! Many thanks and have a great weekend 😄