Running nextflow nfcore pipelines using a singularity

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#1

Hello,

I was wondering if it is possible to run nextflow pipelines from nfcore on a locally installed galaxy server? See examples here Pipelines » nf-core

The nextflow pipelines from nfcore are downloadable as singularities and I have seen some training material on using singularity containers within galaxy Use Singularity containers for running Galaxy jobs

I appreciate there might be a bit of learning curve to get this set up so just wanted to check that this was plausible before I started working through the material.

If anyone can suggest outher training material I might have missed please do let me know

Best wishes
Ollie

#2

Not sure if I can help but I see you dont have an answer yet. If I understand the tutorial correctly it looks like you still need a wrapper to be able to run the workflow from galaxy. I think that galaxy “creates” the container and installs all dependencies in it based on the requirements of the xml wrapper.

Maybe someone else can give a better answer but for now I would guess that you need to make sure you can run the nextflow/singularities workflows from the commandline and make a wrapper yourself around it.

1 Like
#3

Thanks very much for the reply, much appreciated. I will try to run the nexflow singularity from the command line and then try to write a wrapper for it. Will let you know if I have any success!