nextflow kuberun
The kuberun command has been removed. It is available as the nf-kuberun plugin, but it is no longer maintained. See Kubernetes for alternatives.
The kuberun command deployed the Nextflow runtime as a Kubernetes pod, which ran the specified pipeline and submitted each task as a Kubernetes job (or pod).
Migrating to nf-kuberun
To launch a pipeline with the nf-kuberun plugin, replace nextflow kuberun with nextflow plugin nf-kuberun:run. The plugin accepts only double-dash options in the --name=value form, and launcher options such as -c must be given after the command. For example:
# before
nextflow -c my.config kuberun nextflow-io/hello -v my-pvc:/mnt -n my-ns -r master --foo bar
# after
nextflow plugin nf-kuberun:run nextflow-io/hello --config=my.config --volume-mount=my-pvc:/mnt --namespace=my-ns --revision=master --foo=bar
The kuberun options map to the following plugin options:
kuberun option | Plugin option |
|---|---|
-v, -volume-mount | --volume-mount (comma-separated) |
-n, -namespace | --namespace |
-head-image | --head-image |
-head-cpus | --head-cpus |
-head-memory | --head-memory |
-head-prescript | --head-prescript |
-remoteConfig | --remote-config (comma-separated) |
-remoteProfile | --remote-profile |
-c (launcher option) | --config (comma-separated) |
-bg (launcher option) | --background |
The run options supported by kuberun keep their names with a double dash, for example -r becomes --revision and -resume becomes --resume. Short option names such as -r and -w are not supported. See the nf-kuberun README for the full list of options.