HI team Great tool that I love... thanks for the support. I am running some exomes which worked fine before on a different dataset. The pipeline seems to get stuck on the Redux section for no obvious reason (it has an exit code of 0) Tried moving to the directories mentioned in the log and re-executing - they process succesfully but then when I restart the pipeline it crashes out again

Hej! I don’t have an answer for this, but I just recently had the same problem with the WGS mode. Similarly, redux completes with exit code 0 but then the process aborts. I thought it was a Seqera platform related issue, since I could complete the same run without issue on our cluster using native nextflow but it failed when running it via Seqera platform (tower), but then I guess it’s not

Hi everyone, I see you're running v2 of the pipeline, could you try with 2.2 and see if the issue happens again? Additionally, there might be something going on with the Nextflow version.

I did run it on 2.2.0

can you share some logs and configs?

Hi all. I gave up in the end and wrote my own version of the pipeline to make it work. It wasn’t completely clear even with extra debugging in slurm what was going on - the tasks were finishing with exit code 0

Hey Andrew, what do you mean by that?

Just reporting here in case it's useful for someone else, our issue got solved by using the new nextflow version 25.10.0 and disabling NXF_TRACE