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Google Kubernetes Engine

Fusion streamlines the deployment of Nextflow pipelines in Kubernetes because it replaces the need to configure and maintain a shared file system in your cluster.

Platform Google Kubernetes Engine compute environments​

Seqera Platform supports Fusion in Google Kubernetes Engine (GKE) compute environments.

See Google Kubernetes Engine for Platform instructions to enable Fusion.

Nextflow CLI​

note

This feature requires Nextflow 23.02.1-edge or later.

To use Fusion directly in Nextflow with a GKE cluster, you must configure a cluster, namespace, and service account, and update your Nextflow configuration.

Kubernetes configuration​

  1. Create a GKE "standard" cluster ("Autopilot" is not supported). See Creating a zonal cluster for more information.

  2. Use instance types with 2 or more CPUs and SSD storage (families: n1, n2, c2, m1, m2, m3).

  3. Enable the Workload identity feature when creating (or updating) the cluster:

    • Enable Workload Identity in the cluster Security settings.
    • Enable GKE Metadata Server in the node group Security settings.

  4. See Authenticate to Google Cloud APIs from GKE workloads to configure the cluster.

  5. Replace the following example values with values corresponding to your environment:

    • CLUSTER_NAME: the GKE cluster name — cluster-1
    • COMPUTE_REGION: the GKE cluster region — europe-west1
    • NAMESPACE: the GKE namespace — fusion-demo
    • KSA_NAME: the GKE service account name — fusion-sa
    • GSA_NAME: the Google service account — gsa-demo
    • GSA_PROJECT: the Google project id — my-nf-project-261815
    • PROJECT_ID: the Google project id — my-nf-project-261815
    • ROLE_NAME: the role to grant access permissions to the Google Storage bucket — roles/storage.admin

  6. Create the K8s role and rolebinding required to run Nextflow by applying the following Kubernetes config:

    ---
    apiVersion: rbac.authorization.k8s.io/v1
    kind: Role
    metadata:
      namespace: fusion-demo
      name: fusion-role
    rules:
      - apiGroups: [""]
        resources: ["pods", "pods/status", "pods/log", "pods/exec"]
        verbs: ["get", "list", "watch", "create", "delete"]
    ---
    apiVersion: rbac.authorization.k8s.io/v1
    kind: RoleBinding
    metadata:
      namespace: fusion-demo
      name: fusion-rolebind
    roleRef:
      apiGroup: rbac.authorization.k8s.io
      kind: Role
      name: fusion-role
    subjects:
      - kind: ServiceAccount
        name: fusion-sa
    ---
    apiVersion: v1
    kind: Secret
    metadata:
      namespace: fusion-demo
      name: fusion-sa-token
      annotations:
        kubernetes.io/service-account.name: fusion-sa
    type: kubernetes.io/service-account-token
    ...

Nextflow configuration​

  1. Add the following to your nextflow.config file:

    process.executor = 'k8s'
    process.scratch = false
    wave.enabled = true
    fusion.enabled = true
    tower.accessToken = '<PLATFORM_ACCESS_TOKEN>'  
    k8s.context = '<GKE-CLUSTER-CONTEXT>'
    k8s.namespace = 'fusion-demo'
    k8s.serviceAccount = 'fusion-sa'
    k8s.pod.nodeSelector = 'iam.gke.io/gke-metadata-server-enabled=true'

    Replace the following:

    • <PLATFORM_ACCESS_TOKEN>: your Platform access token.
    • <GKE_CLUSTER_CONTEXT>: your Kubernetes configuration context name.

  2. Run the pipeline with the Nextflow run command:

    nextflow run <PIPELINE_SCRIPT> -w gs://<GCS_BUCKET>/work

    Replace the following:

    • <PIPELINE_SCRIPT>: your pipeline Git repository URI.
    • <GCS_BUCKET>: your Google Cloud Storage bucket.
note

When using Fusion, pods will run as privileged by default.

To use Fusion without the need for escalating privileges, install the Nextflow FUSE device plugin on your Kubernetes cluster and add set fusion.privileged to false in your nextflow.config file:

fusion.privileged = false

To use a custom FUSE device plugin, specify it via the k8s.fuseDevicePlugin configuration option. See Kubernetes configuration options for details.