nextflow-io/nextflow

AWS Batch Fargate requires exact CPU values?

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#5,781 opened on Feb 12, 2025

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 (4 comments) (0 reactions) (0 assignees)Groovy (3,382 stars) (784 forks)batch import
executor/aws-batchgood first issue

Description

When running wf-human-variation from ONT on AWSBatch Fargate, I get this error

ERROR ~ Error executing process > 'ingress:minimap2_alignment (1)'

Caused by:
  Requirement of 12 CPUs is not allowed by Fargate -- Check process with name 'ingress:minimap2_alignment (1)'

From what I can tell it's because the requested CPU value does not match one from the list found here:

https://github.com/nextflow-io/nextflow/blob/944f48f9b52d47032bf57e16cfe11fe9410972b2/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy#L923-L943

It seems a bit restrictive to require specific CPU values, am I doing something wrong or is that in fact the case?

Contributor guide

Tech stack
groovyaws
Domain
backendcloudinfrastructure
Issue type
bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-2 days
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
mostly clear
Prerequisites
AWS BatchFargateGroovy programming
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
30
Research direction
The issue points to a specific file in the Nextflow AWS Batch plugin: AwsBatchTaskHandler.groovy, lines 923-943, which defines a list of allowed CPU values for Fargate. The error occurs because the process requires 12 CPUs, which is not in that list. A potential fix would be either to adjust the process CPU request to a valid Fargate value, or to modify the plugin to automatically round up to the nearest allowed value (if permitted by AWS). The issue is clear and well documented, and no linked PRs exist yet.