Modified on Mon, 19 Sep 2022 at 03:15 AM

Q: How do I make my Nextflow pipelines more resilient to VM preemption?

Running your pipelines on Preemptible VMs (PVMs) provides significant cost savings, but increases the likelihood that a task will be interrupted before completion. It is a recommended best practice to implement a retry strategy when you encounter exit codes that are commonly related to preemption. Example: 

process {
  errorStrategy = { task.exitStatus in [8,10,14] ? 'retry' : 'finish' }
  maxRetries    = 3
  maxErrors     = '-1'

Q: What are the minimum Tower service account permissions needed for GLS and GKE?

The following roles need to be granted to the nextflow-service-account:

  1. Cloud Life Sciences Workflows Runner
  2. Service Account User
  3. Service Usage Consumer
  4. Storage Object Admin

For detailed information, please refer to this guide.

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