Kubernetes is a cloud-native open-source system for deployment, scaling, and management of containerized applications.
It provides clustering and file system abstractions that allows the execution of containerised workloads across different cloud platforms and on-premises installations.
The built-in support for Kubernetes provided by Nextflow streamlines the execution of containerised workflows in Kubernetes clusters.
Kubernetes main abstraction is the
pod defines the (desired) state of one or more containers i.e. required computing resources, storage, network configuration.
Kubernetes abstracts also the storage provisioning through the definition of one more persistent volumes that allow containers to access to the underlying storage systems in a transparent and portable manner.
When using the
k8s executor Nextflow deploys the workflow execution as a Kubernetes pod. This pod orchestrates the workflow execution and submits a separate pod execution for each job that need to be carried out by the workflow application.
Such volume needs to be accessible through a Persistent Volume Claim, which will be used by Nextflow to run the application and store the scratch data and the pipeline final result.
The workflow application has to be containerised using the usual Nextflow container directive.
When using Wave containers and Fusion file system there is no need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes. You can ignore this requirement when using the Fusion file system. See the Fusion file system documentation for further details.
The workflow execution needs to be submitted from a computer able to connect to the Kubernetes cluster.
Nextflow uses the Kubernetes configuration file available at the path
$HOME/.kube/config or the file specified by the environment variable
You can verify such configuration with the command below:
$ kubectl cluster-info
Kubernetes master is running at https://your-host:6443
KubeDNS is running at https://your-host:6443/api/v1/namespaces/kube-system/services/kube-dns:dns/proxy
kuberun is considered an obsolete approach for the deployment of Nextflow pipeline with Kubernetes and is no longer maintained. For a better alternative, consider using Launch with Fusion.
To deploy and launch the workflow execution use the Nextflow command
kuberun as shown below:
nextflow kuberun <pipeline-name> -v vol-claim:/mount/path
This command will create and execute a pod running the nextflow orchestrator for the specified workflow. In the above example replace
<pipeline-name> with an existing nextflow project or the absolute path of a workflow already deployed in the Kubernetes cluster.
-v command line option is required to specify the volume claim name and mount path to use for the workflow execution. In the above example replace
vol-claim with the name of an existing persistent volume claim and
/mount/path with the path where the volume is required to be mount in the container. Volume claims can also be specified in the Nextflow configuration file, see the Kubernetes configuration section for details.
Once the pod execution starts, the application in the foreground prints the console output produced by the running workflow pod.
For debugging purpose it’s possible to execute a Nextflow pod and launch an interactive shell using the following command:
nextflow kuberun login -v vol-claim:/mount/path
This command creates a pod, sets up the volume claim(s), configures the Nextflow environment and finally launches a Bash login session.
The pod is automatically destroyed once the shell session terminates. Do not use it to launch long-running workflows in the background.
Launch with Fusion
New in version 22.10.0.
The use of Fusion file system allows deploying a Nextflow pipeline to a remote (or local) cluster without the need to use a shared file system and configure a persistent volume claim for the deployment of Nextflow pipeline with Kubernetes.
This also makes unnecessary the use of the special
kuberun command for the pipeline execution.
For this deployment scenario the following configuration can be used:
enabled = true
enabled = true
executor = 'k8s'
context = '<YOUR K8S CONFIGURATION CONTEXT>'
namespace = '<YOUR K8S NAMESPACE>'
serviceAccount = '<YOUR K8S SERVICE ACCOUNT>'
k8s.context represents the Kubernetes configuration context to be used for the pipeline execution. This setting can be omitted if Nextflow itself is run as a pod in the Kubernetes cluster.
k8s.namespace represents the Kubernetes namespace where the jobs submitted by the pipeline execution should be executed.
k8s.serviceAccount represents the Kubernetes service account that should be used to grant the execution permission to jobs launched by Nextflow. You can find more details how to configure it as the following link.
Then the pipeline execution can be launched using the usual run command and specifying a AWS S3 bucket work directory, for example:
nextflow run <YOUR PIPELINE> -work-dir s3://<YOUR-BUCKET>/scratch
Running in a pod
Nextflow can be executed directly from a pod running in a Kubernetes cluster. In these cases you will need to use the plain Nextflow
run command and specify the
k8s executor and the required persistent volume claim in the
nextflow.config file as shown below:
executor = 'k8s'
storageClaimName = 'vol-claim'
storageMountPath = '/mount/path'
storageSubPath = '/my-data'
In the above snippet replace
vol-claim with the name of an existing persistent volume claim and replace
/mount/path with the actual desired mount path (default:
storageSubPath with the directory in the volume to be mounted (default:
The running pod must have been created with the same persistent volume claim name and mount as the one specified in your Nextflow configuration file. Note also that the
run command does not support the
It is also possible to mount multiple volumes using the
pod directive, for example:
k8s.pod = [ [volumeClaim: "other-pvc", mountPath: "/other" ]]
The process pod directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. See the pod directive for more details.
kuberun command does not allow the execution of local Nextflow scripts. It is only intended as a convenient way to test the deployment of pipelines to a Kubernetes cluster.