Docker vs Nextflow

[DrDee79]

I am having issues as I can't run Docker on my laptop and our big processing machine is running Windows Server (it's a VM) which won't run Docker without $$$. Is there a way to get into Nextflow or something similar that can run on this option?

[trishorts]

You can actually put docker containers inside of nextflow. We do that here with a MetaMorpheus docker https://github.com/sheynkman-lab/Long-Read-Proteogenomics

I'm don't think that we have the human resources available to do that at the moment. But if you know someone familiar with Nextflow, this should be pretty straightforward.

[DrDee79]

Thank you this is great! I think several people in our comp sci work with Nextflow which is why I mentioned it.

[trishorts]

I havent' done this myself. But, I think you need to make sure that you provide a directory that the docker can write to for its output when you put this all inside of nextflow. And, I think the docker may be at a directly level below what you imagine it to be. I'm probably talking nonsense, but maybe you can share this with your nextflow people and they will understand what I mean.

[acesnik]

Hi there, you can also run Spritz on the commandline, and I've updated it today, so that it's able to run on protected-access servers without open internet access. That might be an option here.