Nextflow · Cromwell · AWS Batch · GCP Cloud Batch
Your pipelines. Your cloud account.Your bill, itemised.
GENI Workflows is a control plane for genomics pipelines. You get one API and one CLI across every account and both clouds; the sequencing data and the compute never leave the accounts you already own.
npm install -g geni-bioinfo- succeeded
- running
- queued
- reclaimed
Cloud genomics gets expensive in two directions
Running Nextflow or Cromwell on cloud infrastructure yourself means owning Batch compute environments, IAM, image registries, spot interruptions and retry logic — per account, per region, forever. Every new client account starts that work again.
Managed services remove that work and charge for it. And when the invoice arrives at the end of the month, it is one number for the whole account: no answer to which workflow, which sample or which client it came from.
What you manage
Six objects, both clouds
The same six resources describe an AWS account and a GCP project. Learn them once.
- Environment
- An AWS account or GCP project, plus a region. Register as many as you run in — dev, prod, one per client.
- Engine
- Runs Nextflow or Cromwell for each submission, scoped to the exact buckets it is allowed to read and write.
- Queue
- Where tasks execute, on AWS Batch or GCP Cloud Batch. Keep a spot queue and an on-demand queue; pick one per run.
- Storage
- S3 and GCS buckets, whether GENI created them or they already existed in your account.
- Registry
- Your ECR repositories. Engines in an environment can pull the images you built for your own tools.
- Plugins
- Optional per-environment extras — a Sentieon license server, an SNS topic for submission status changes.
Cost
Every run has a price on it
GENI reconciles against the AWS Cost and Usage Report and the GCP FOCUS billing export — actual billed cost, not an estimate from a price list. Attribute it by workflow, environment, queue, instance type, or by the tags you put on a submission.
How tagging works| client | runs | billed |
|---|---|---|
| acme | 128 | $1,204.60 |
| hospital-sp | 74 | $688.12 |
| research-x | 31 | $294.05 |
| validation | 12 | $71.88 |
Start with the CLI
Install it, activate the account your admin created, and list what is already running.
npm install -g geni-bioinfo
geni auth activate --token <token from email>
geni submission list