Snakemake executor plugin: kubernetes

Warning

No documentation found in repository https://github.com/snakemake/snakemake-executor-plugin-kubernetes. The plugin should provide a docs/intro.md with some introductory sentences and optionally a docs/further.md file with details beyond the auto-generated usage instractions presented in this catalog.

Installation

Install this plugin by installing it with pip or mamba, e.g.:

pip install snakemake-executor-plugin-kubernetes

Usage

In order to use the plugin, run Snakemake (>=8.0) with the corresponding value for the executor flag:

snakemake --executor kubernetes ...

with ... being any additional arguments you want to use.

The executor plugin has the following settings:

Settings

CLI argument	Description	Default	Choices	Required	Type
--kubernetes-namespace VALUE	The namespace to use for submitted jobs.	'default'		✗
--kubernetes-cpu-scalar VALUE	K8s reserves some proportion of available CPUs for its own use. So, where an underlying node may have 8 CPUs, only e.g. 7600 milliCPUs are allocatable to k8s pods (i.e. snakemake jobs). As 8 > 7.6, k8s can’t find a node with enough CPU resource to run such jobs. This argument acts as a global scalar on each job’s CPU request, so that e.g. a job whose rule definition asks for 8 CPUs will request 7600m CPUs from k8s, allowing it to utilise one entire node. N.B: the job itself would still see the original value, i.e. as the value substituted in {threads}.	0.95		✗
--kubernetes-service-account-name VALUE	This argument allows the use of customer service accounts for kubernetes pods. If specified, serviceAccountName will be added to the pod specs. This is e.g. needed when using workload identity which is enforced when using Google Cloud GKE Autopilot.	None		✗
--kubernetes-privileged VALUE	Create privileged containers for jobs.	False		✗
--kubernetes-persistent-volumes VALUE	Mount the given persistent volumes under the given paths in each job container (<name>:<path>).	None		✗