We currently support custom resources in Serial, Yadage and CWL workflow:
kubernetes_uid
kubernetes_memory_limit
htcondor_max_runtime
...
For instance, one can see how to enable kubernetes_memory_limit in the different workflow languages here.
Expected behavior
The goal of this task is to find a way to pass custom resources to each Snakemake rule via Snakefile, to be able to read them at a workflow engine level and be used by the job controller subsequently.
We must find a way to pass custom values in the Snakefile, same as Yadage does with step.environment.resources and CWL does with hints.reana.
Afterward, test that the passed custom resources work as expected when running workflows in the cluster.
Current behavior
We currently support custom resources in Serial, Yadage and CWL workflow:
kubernetes_uidkubernetes_memory_limithtcondor_max_runtimeFor instance, one can see how to enable
kubernetes_memory_limitin the different workflow languages here.Expected behavior
The goal of this task is to find a way to pass custom resources to each Snakemake rule via Snakefile, to be able to read them at a workflow engine level and be used by the job controller subsequently.
We must find a way to pass custom values in the Snakefile, same as Yadage does with
step.environment.resourcesand CWL does withhints.reana.Afterward, test that the passed custom resources work as expected when running workflows in the cluster.
PS. FIXME: https://github.com/reanahub/reana-commons/blob/bad177fffc332c72440f310a77fc2e3d6b6f69ef/reana_commons/snakemake.py#L68