Hi! I'm running into an issue with the pdc_kth profile I believe. I've previously been running amliseq through Nextflow on Dardel without issues, but when trying to run the following:

nextflow run nf-core/ampliseq \
-profile pdc_kth \
-r 2.17.0 \
-params-file params.yaml \
-bg

I get the following error message. Has there been any changes to the PDC profile config file, or what could be the reason? Thanks in advance! 🙏

Error nextflow.config:26:23: Unexpected input: '\n'
? 26 |     case "dardel":
?   |            ^
ERROR ~ Config parsing failed

We should no longer have

case

but if blocks with the strict syntax. I thought we fixed that

I'm sorry but I don't know what that means? Is it something I can specify/correct on my end?

Sorry, what version of Nextflow are you using?

Trying to call 2.17.0 with this command -r 2.17.0 \ But the loaded module is version 26.04.3 build 12259

-r would be for the pipeline version, so that should be good

Then it works! Thank you!

There have been changes to the dardel config recently by me, but that should not affect what you're doing. Are you using a local copy of the config (there is no need to but I see a lot of people doing this)? This is what the current pdc_kth.config looks like: github.com/nf-core/configs/blob/…/pdc_kth.config. There's no

case

in there, so I'm not sure where that's coming from.

I had to try now, and I can at least start ampliseq 2.17.0 with

test,pdc_kth

profiles under 26.04.3, so I suspect this is a file stashed somewhere.

I actually don't know if I have that as a local file, it's quite long ago I set it up and simply don't remember. Is there a way you recommend me to check it? Things are running smootlhly now when I specified an earlier nextflow version. Thanks for the help! Much appreciated.

Where you run the

nextflow run

command, do you have config files there? The

.nextflow.log

in that directory ( hidden file - so make it appear with

ls -la

), has near the top of the log what the command-line call you used was, and then lower down, which config files were loaded. In your case, since

nextflow

is running smoothly, you'll need to check one of the older logs like

.nextflow.log.1

which would be the previous run, and

.2

was before that.

If you don't need anything more that will require a refreshed version you can probably leave it. If you want to figure it out, it's probably

nextfliow.config

either in your home directory or where you run.