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Version: 24.2

Google GKE

Google Kubernetes Engine (GKE) is a managed Kubernetes cluster that allows the execution of containerized workloads in Google Cloud at scale.

Seqera Platform offers native support for GKE clusters to streamline the deployment of Nextflow pipelines.

Requirements​

See here for instructions to set up your Google Cloud account and other services (such as Cloud storage).

You must have a GKE cluster up and running. Follow the cluster preparation instructions to create the resources required by Seqera. In addition to the generic Kubernetes instructions, you must make a number of modifications specific to GKE.

Service account role​

You must grant cluster access to the service account used by the Seqera compute environment. To do this, update the service account RoleBinding:

cat << EOF | kubectl apply -f -
---
apiVersion: rbac.authorization.k8s.io/v1
kind: RoleBinding
metadata:
    name: tower-launcher-userbind
subjects:
    - kind: User
    name: <IAM SERVICE ACCOUNT>
    apiGroup: rbac.authorization.k8s.io
roleRef:
    kind: Role
    name: tower-launcher-role
    apiGroup: rbac.authorization.k8s.io
---
EOF

Replace <IAM SERVICE ACCOUNT> with the corresponding service account, e.g., test-account@test-project-123456.google.com.iam.gserviceaccount.com.

See Role-based access control for more information.

Seqera compute environment​

Your Seqera compute environment uses resources that you may be charged for in your Google Cloud account. See Cloud costs for guidelines to manage cloud resources effectively and prevent unexpected costs.

After you've prepared your Kubernetes cluster and granted cluster access to your service account, create a Seqera GKE compute environment:

  1. In a Seqera workspace, select Compute environments > New environment.

  2. Enter a descriptive name for this environment, e.g., Google GKE (europe-west1).

  3. From the Provider drop-down, select Google GKE.

  4. Under Storage, select either Fusion storage (recommended) or Legacy storage. The Fusion v2 virtual distributed file system allows access to your Google Cloud-hosted data (gs:// URLs). This eliminates the need to configure a shared file system in your Kubernetes cluster. See Fusion v2 below.

  5. From the Credentials drop-down menu, select existing GKE credentials, or select + to add new credentials. If you choose to use existing credentials, skip to step 8.

  6. Enter a name for the credentials, e.g., GKE Credentials.

  7. Enter the Service account key for your Google service account.

    You can create multiple credentials in your Seqera environment. See Credentials.

  8. Select the Location of your GKE cluster.

    GKE clusters can be either regional or zonal. For example, us-west1 identifies the United States West-Coast region, which has three zones: us-west1-a, us-west1-b, and us-west1-c.

    Seqera Platform's auto-completion only shows regions. You should manually edit this field if you're using a zonal GKE cluster.

  9. Select or enter the Cluster name of your GKE cluster.

  10. Specify the Namespace created in the cluster preparation instructions. This is tower-nf by default.

  11. Specify the Head service account created in the cluster preparation instructions. This is tower-launcher-sa by default.

    If you enable Fusion v2 (Fusion storage in step 4 above), the head service account must have access to the Google Cloud storage bucket specified as your work directory.

  12. Specify the Storage claim created in the cluster preparation instructions. This serves as a scratch filesystem for Nextflow pipelines. The storage claim is called tower-scratch in the provided examples.

    The Storage claim isn't needed when Fusion v2 is enabled.

  13. Apply Resource labels to the cloud resources consumed by this compute environment. Workspace default resource labels are prefilled.

  14. Expand Staging options to include:

    • Optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment.
    • Global Nextflow configuration settings for all pipeline runs launched with this compute environment. Values defined here are pre-filled in the Nextflow config file field in the pipeline launch form. These values can be overridden during pipeline launch.

    Configuration settings in this field override the same values in the pipeline repository nextflow.config file. See Nextflow config file for more information on configuration priority.

  15. Specify custom Environment variables for the Head job and/or Compute jobs.

  16. Configure any advanced options described in the next section, as needed.

  17. Select Create to finalize the compute environment setup.

Advanced options​

Seqera Platform compute environments for GKE include advanced options for storage and work directory paths, resource allocation, and pod customization.

  • The Storage mount path is the file system path where the Storage claim is mounted (default: /scratch).
  • The Work directory is the file system path used as a working directory by Nextflow pipelines. It must be the storage mount path (default) or a subdirectory of it.
  • The Compute service account is the service account used by Nextflow to submit tasks (default: the default account in the given namespace).
  • The Pod cleanup policy determines when to delete terminated pods.
  • Use Custom head pod specs to provide custom options for the Nextflow workflow pod (nodeSelector, affinity, etc). For example:
spec:
    nodeSelector:
    disktype: ssd
  • Use Custom service pod specs to provide custom options for the compute environment pod. See above for an example.
  • Use Head Job CPUs and Head Job Memory to specify the hardware resources allocated for the Nextflow workflow pod.

See Launch pipelines to start executing workflows in your GKE compute environment.

Fusion v2​

To use Fusion v2 in your Seqera GKE compute environment:

  1. Use Seqera Platform version 23.1 or later.
  2. Use an S3 bucket as the pipeline work directory.
  3. Both the head service and compute service accounts must have access to the Google Cloud storage bucket specified as the work directory.
Configure IAM to use Fusion v2
  1. Ensure the Workload Identity feature is enabled for the cluster:
    • Enable Workload Identity in the cluster Security settings.
    • Enable GKE Metadata Server in the node group Security settings.
  2. Allow the IAM service account access to your Google storage bucket: 
    gcloud storage buckets add-iam-policy-binding gs://<YOUR-BUCKET> --role roles/storage.objectAdmin --member serviceAccount:<IAM-SERVICE-ACCOUNT>@<GOOGLE-CLOUD-PROJECT>.iam.gserviceaccount.com
    The role must have at least storage.objects.create, storage.objects.get, and storage.objects.list permissions.
  3. Allow the Kubernetes service account to impersonate the IAM service account: 
    gcloud iam service-accounts add-iam-policy-binding <IAM-SERVICE-ACCOUNT>@<GOOGLE-CLOUD-PROJECT>.iam.gserviceaccount.com --role roles/iam.workloadIdentityUser --member "serviceAccount:<GOOGLE-CLOUD-PROJECT>.svc.id.goog[<GKE-NAMESPACE>/<GKE-SERVICE-ACCOUNT>]"
  4. Annotate the Kubernetes service account with the email address of the IAM service account: 
    kubectl annotate serviceaccount <GKE-SERVICE-ACCOUNT> --namespace <GKE-NAMESPACE> iam.gke.io/gcp-service-account=<IAM-SERVICE-ACCOUNT>@<GOOGLE-CLOUD-PROJECT>.iam.gserviceaccount.com

See the GKE documentation for further details.