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
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.
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!
@Ollie_White were you able to get this up and running? I’m working on this same problem now and struggling. Nextflow just seems to hang before any of the pipeline steps are run. Thanks!
Hi @aveltri I have got nextflow singularities to run on the command line and I have been teaching myself how to write galaxy xml wrappers recently. My plan is to start writing galaxy wrappers for a nextflow pipeline, specifically ampliseq https://nf-co.re/ampliseq. I will let you know how it goes if it is of interest to you?
Hey @Ollie_White, I’m in the same boat teaching myself to do this as well. I can run Nextflow outside of Galaxy, and I can run my own xml wrapped tools inside Galaxy, but when I combine the two (Nextflow in a Galaxy xml wrapper), I can see in the logs that Nextflow never executes any of the workflow steps and just stalls. I can’t even get nextflow run hello to work, so I’m not sure if this is a bug in Galaxy or Nextflow or just something about my configuration. Ultimately I’m interested in getting a few of the nf-core pipelines to run as well, including RNA-seq and CHIP-seq, but right now I’m resorting to rebuilding pipelines as Galaxy workflows.
Please do let me know your how it works out for you. I would be happy to share my XML files or any other resources if you’d like to test them in your Galaxy instance.
Hi @Ollie_White, I noticed your post about working with nf-core pipelines in Galaxy. I’m particularly interested in wrapping the nf-core/ampliseq pipeline.
I was wondering if you managed to successfully write a proper XML file for this or any other pipeline and if you could share your experience or any tips you might have. It would be really helpful as I work on this.