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pod

The pod directive defines pod-specific settings, such as environment variables, secrets, and config maps, when using the Kubernetes executor.

For example:

process echo {
    pod env: 'MESSAGE', value: 'hello world'

    script:
    """
    echo $MESSAGE
    """
}

The above snippet defines an environment variable named MESSAGE whose value is 'hello world'.

Pod settings can be specified in Nextflow configuration:

// single setting
process.pod = [env: 'MESSAGE', value: 'hello world']

// multiple settings
process.pod = [
    [env: 'MESSAGE', value: 'hello world'],
    [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
]

The following options are available:

affinity: <config>​

Specifies the pod affinity with the given configuration.

annotation: '<name>', value: '<value>'​

Can be specified multiple times

Defines a pod annotation with the given name and value.

automountServiceAccountToken: true | false​

Specifies whether to automount service account token into the pod (default: true).

config: '<configMap>/<key>', mountPath: '</absolute/path>'​

Can be specified multiple times

Mounts a ConfigMap with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the ConfigMap are exposed in that path.

csi: '<config>', mountPath: '</absolute/path>'​

Can be specified multiple times

Mounts a CSI ephemeral volume with the given configuration to the given path.

emptyDir: <config>, mountPath: '</absolute/path>'​

Can be specified multiple times

Mounts an emptyDir with the given configuration to the given path.

env: '<name>', config: '<configMap>/<key>'​

Can be specified multiple times

Defines an environment variable whose value is defined by the given ConfigMap and key.

env: '<name>', fieldPath: '<fieldPath>'​

Can be specified multiple times

Defines an environment variable whose value is defined by the given field path value.

For example, the following pod option:

process.pod = [env: 'MY_NODE_NAME', fieldPath: 'spec.nodeName']

Maps to the following pod spec:

env:
  - name: MY_NODE_NAME
    valueFrom:
      fieldRef:
        fieldPath: spec.nodeName
env: '<name>', secret: '<secret>/<key>'​

Can be specified multiple times

Defines an environment variable whose value is defined by the given Secret and key.

env: '<name>', value: '<value>'​

Can be specified multiple times

Defines an environment variable with the given name and value.

hostPath: '/host/absolute/path', mountPath: '</pod/absolute/path>'​
Added in version 23.10

Can be specified multiple times

Allows creating hostPath volume and access it with the specified mountPath in the pod.

imagePullPolicy: 'IfNotPresent' | 'Always' | 'Never'​

Specifies the image pull policy used by the pod to pull the container image.

imagePullSecret: '<name>'​

Specifies the image pull secret used to access a private container image registry.

label: '<name>', value: '<value>'​

Can be specified multiple times

Defines a pod label with the given name and value.

nodeSelector: <config>​

Specifies the node selector with the given configuration.

The configuration can be a map or a string:

// map
process.pod = [nodeSelector: [disktype: 'ssd', cpu: 'intel']]

// string
process.pod = [nodeSelector: 'disktype=ssd,cpu=intel']
priorityClassName: '<name>'​

Specifies the priority class name for pods.

privileged: true | false​

Specifies whether the pod should run as a privileged container (default: false).

runAsUser: '<uid>'​

Specifies the user ID with which to run the container. Shortcut for the securityContext option.

runtimeClassName: '<name>'​

Specifies the runtime class.

schedulerName: '<name>'​

Specifies which scheduler is used to schedule the container.

secret: '<secret>/<key>', mountPath: '</absolute/path>'​

Can be specified multiple times

Mounts a Secret with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the Secret are exposed in that path.

securityContext: <config>​

Specifies the pod security context with the given configuration.

toleration: <config>​

Can be specified multiple times

Specifies the pod toleration with the given configuration.

The configuration should be a map corresponding to a single toleration rule. For example, the following pod options:

process.pod = [
    [toleration: [key: 'key1', operator: 'Equal', value: 'value1', effect: 'NoSchedule']],
    [toleration: [key: 'key1', operator: 'Exists', effect: 'NoSchedule']],
]

Maps to the following pod spec:

tolerations:
  - key: "key1"
    operator: "Equal"
    value: "value1"
    effect: "NoSchedule"
  - key: "key1"
    operator: "Exists"
    effect: "NoSchedule"
ttlSecondsAfterFinished​
Added in version 24.04

Specifies the TTL mechanism for finished jobs in seconds. Applies to both successful and failed jobs.

volumeClaim: '<name>', mountPath: '</absolute/path>' [, subPath: '<path>', readOnly: true | false]​

Can be specified multiple times

Mounts a Persistent volume claim with the given name to the given path.

The subPath option can be used to mount a sub-directory of the volume instead of its root.

The readOnly option can be used to mount the volume as read-only (default: false)

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