We are trying to run Snakemake workflows on Kubernetes on premise infrastructure. We are using OpenShift OKD on a MapR filesystem more precisely.

We followed the official documentation command:

snakemake --kubernetes --use-conda --default-remote-provider $REMOTE --default-remote-prefix $PREFIX

But the command line help provided for --default-remote-provider and --default-remote-prefix are not clear about how we should execute Snakemake pipelines on a on premise Kubernetes or OpenShift cluster:

--default-remote-provider: choose from 'S3', 'GS', 'FTP', 'SFTP', 'S3Mocked', 'gfal', 'gridftp', 'iRODS'

Also, the official documentation states:

In this mode, Snakemake will assume all input and output files to be stored in a given remote location, configured by setting $REMOTE to your provider of choice (e.g. GS for Google cloud storage or S3 for Amazon S3) and $PREFIX to a bucket name or subfolder within that remote storage.

So I was wondering:

• How does one should proceed to deploy Snakemake workflow to on premise OpenShift/Kubernetes installation?

• Is there example (such as github repo or blog) of running Snakemake on premise clusters?

• In particular, I am not sure which remote provider should be chosen, and how to provide the prefix (can it be linked to a Kubernetes Persistent Volume Claim?)

Thanks a lot for your help!