Hello, I've been using nf-core pipelines on Dardel by running this before the pipeline: pixi shell screen -S name module load PDC apptainer It has been working for a while, but now this happens: (base) nicolai2@login1:/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis> pixi shell WARNING: Did not detect successful shell initialization within 3 second(s). Please check on https://pixi.sh/latest/advanced/pixi_shell/#issues-with-pixi-shell for more tips. . /tmp/pixi_env_sAH.sh (base) nicolai2@login1:/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_aalysis> . /tmp/pixi_env_sAH.sh PIXI_SHELL_ACTIVATION_DONE (ampliseq_analysis) (base) nicolai2@login1:/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis> Does anyone have the same problem? Are there other ways and modules to load nextflow, so I can run the ampliseq pipeline? Kind regards, Nicolai

I can't test now but it seems your problem is with pixi and can easily be avoided by not requiring pixi, e.g. by following the docs at https://github.com/nf-core/configs/blob/master/docs/pdc_kth.md

Thanks!

I found it quite common to experience that message, but it didn't really mean anything. It just means it took a bit longer to load the shell. You should still be able to run as normal. I would usually run

screen

first, and then do

pixi shell

or

pixi run

. I also have a script called

run_nextflow.sh

that not only calls nextflow, but cleans any redundant work dirs afterwards. If you're interested in it, it's here: https://github.com/NBISweden/assembly-project-template/blob/main/analyses/01_ebp-assembly-workflow/run_nextflow.sh If there's anything you want to know about it, feel free to ask.