I am running into issues setting up the config files. Would anyone be able to assist me? FYI, I am trying to run a huge dataset of co-assemblies in hybrid mode on a HPC at the Helmholtz Center for Environmental Research - UFZ. So the configuration of resources is somewhat confusing me since I have to submit a slurm submission script

Happy to help (I'm on the other side of Leipzig even 😉 ) In the meantime, have you tried following this tutorail: https://nf-co.re/docs/tutorials/use_nf-core_pipelines/writing_institutional_profiles If by 'configuring' the pipeline you mean getting it to work on the HPC vs. setting the write parameters

Hi James, Thanks a bunch for the quick reply. Would it be possible to set up a zoom meeting? Maybe it would be quicker to clarify some issues. There is a lot of documentation to go through 🙂

I'm very busy this week unfortunately, lots of meetings and running a workshop thurs/friday

No worries James (I also have to give a phage workflow tutorial for the next 3 days) 🙂. Depending on the time I might be able to join the weekly helpdesk. In the meantime would it be possible to send you personally my scripts and config files for you to have a look at once you have time? I know I'm being a bit annoying but would love to have this workflow up and running.

Sure, send me the scripts/config file, and the problem you're having

Also, I think I might need to rethink my strategy for this specific project. I have 36 samples of both short and long reads. They are quite big files and I would like to have a hybrid co-assembly but the resources required would be humongous. Short read folder amounts to 74Gb and long reads = 103Gb

OK, That I can't really comment on

I sometimes get resource errors. So I guess it's mostly about setting up the config file and making sure it doesn'T conflict with the actual submission script to the slurm HPC

I think reading the documnetation page I linked above will help you a lot with that 😉

I have to admit that I'm not versed on nextflow so it takes me while 🙂

But we should really make a separate config for the HPC specifically https://github.com/nf-core/configs/

Hi James. First of all happy new year!

Not that I'm aware of. But I think other than maybe a couple of binners none of the tools re designed for GPU/do not have GPU modes anyway...