Hi this is a bug report I tried searching for other channels nf-core #help

Hi, this is a bug report. I tried searching for ot...

Paul Petrowski

07/20/2026, 9:43 PM

Hi, this is a bug report. I tried searching for other channels to put this in but found no other obvious candidates so I'm defaulting to here. Please redirect me if appropriate. I have a fresh conda env containing nextflow v26.04.6, nf-core v4.0.2 and python v3.14.6. I tried

nf-core pipelines launch nf-core/rnaseq -r 3.26.0

. This produced the error found in the attached txt file. I also tried replacing rnaseq with sarek, and this produced the same result. Given the fresh install, repeatable nature across pipelines, and latest versions of everything, I believe this is a genuine bug. Thanks!

Thomas Danhorn

07/21/2026, 2:30 AM

What are you trying to do? Would

nextflow run nf-core/rnaseq -r 3.26.0 <other parameters>

do what you want?

Thomas Danhorn

07/21/2026, 3:16 AM

If you want a GUI to create a JSON file to use with

-params-file

, you can use the web interface (go to nf-co.re/rnaseq/3.26.0 and press the "Launch" button, enter your parameters, copy the output to a file and use that in the command).

Thomas Danhorn

07/21/2026, 3:26 AM

There have been lots of fundamental changes (strict syntax) in Nextflow as well as the various pipelines lately, so it is quite possible that some of those have broken things in the

nf-core

tool. (If you are curious, you can get some older versions of Nextflow and/or the tool and test. The

launch

function works from the website, but I don't know which versions of everything they are using there.) If you are interested in discussing that, the #CE5LG7WMB channel would be the best place. For a simple bug report, you can go to GitHub (make sure there is not already one similar to this).

pontus

07/21/2026, 6:37 AM

It does look like a bug in that it should probably give a more helpful error message on bad calling (but as Thomas implies, calling like that isn't expected). But the best place to report such things is the repository Thomas linked to above.

Paul Petrowski

07/21/2026, 5:09 PM

I see, the posted link to the param builder is what I was going for. (A bit new to nf-core so appreciate the patience). Agree that a more informative error message in this case would be helpful. Guess I was under the impression that the command I posted would launch the param builder

Phil Ewels

08/14/2026, 12:29 PM

You should never get an unhandled traceback like this from nf-core/tools, if you do then I class it as a bug

Phil Ewels

08/14/2026, 12:29 PM

Best to report in #CE5LG7WMB - that's the slack channel for the nf-core CLI

Paul Petrowski

08/14/2026, 11:41 PM

Thanks, I'll move it over to #CE5LG7WMB.

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