minicluster.yaml

apiVersion: flux-framework.org/v1alpha1
kind: MiniCluster
metadata:
  name: flux-sample
  namespace: flux-operator
spec:

  # Number of pods to create for MiniCluster
  size: 2

  # Cleanup the storage volume (PVC and PV) after run
  cleanup: true

  # suppress all output except for test run
  logging:
    quiet: true

  # Make this kind of persistent volume and claim available to pods
  # This is a path in minikube (e.g., minikube ssh)
  volumes:
    data:
      storageClass: hostpath
      path: /tmp/data

  # This is a list because a pod can support multiple containers
  containers:

      # This image has snakemake installed, and although it has data, we will
      # provide it as a volume to the container to demonstrate that (and share it)
    - image: ghcr.io/rse-ops/atacseq:app-latest

      # We are saying to mount the "data" volume defined above to "/workflow"
      # in the container
      volumes:
        data:
          path: /tmp/data
          # readOnly defaults to false

      # This is the directory we will bind the data to
      workingDir: /tmp/data
      command: snakemake --cores 1 --flux --jobs 1

      # Give the command directly to flux start, instead of wrapping in flux submit
      launcher: true
      preCommand: |
        # Ensure the cache targets our flux user home
        asFlux="sudo -u flux -E PYTHONPATH=$PYTHONPATH -E PATH=$PATH -E HOME=/home/flux"
        # Add the flux user beforehand, and ensure we own the working directory with data
        sudo adduser --disabled-password --uid 1000 --gecos "" flux > /dev/null 2>&1