Summary

nf-kuberun is a Nextflow plugin that launches a pipeline in a Kubernetes cluster, with the Nextflow driver itself running in a pod. It replaces the nextflow kuberun command, which was removed from Nextflow in version 27.04.

Get Started

Basic Usage

nextflow plugin nf-kuberun:run <pipeline> [script args] [--option=value ...]

Example Configuration

nextflow plugin nf-kuberun:run nextflow-io/hello --namespace=my-ns --volume-mount=my-pvc:/mnt/data

Setup

The plugin depends on the nf-k8s plugin, which is installed automatically. Configure the cluster connection and storage with the k8s config scope.

Important notes:

• The pipeline must be a remote Git project or the absolute path of a project already deployed in the cluster
• Local scripts are not supported
• Use login as the pipeline name to launch an interactive driver pod and attach to it with kubectl
• Options are given with a double dash in the form --name=value
• Options that take multiple values accept a comma-separated list

Examples

Simple Pipeline Execution

nextflow plugin nf-kuberun:run nextflow-io/hello --namespace=my-ns

With Volume Mounts and Configuration

nextflow plugin nf-kuberun:run nextflow-io/hello \
  --config=my.config \
  --volume-mount=my-pvc:/mnt \
  --revision=master \
  --foo=bar

Interactive Driver Pod

nextflow plugin nf-kuberun:run login

Then attach with:

kubectl attach <pod-name> -i -t

License

This project is licensed under the Apache License 2.0.