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Cannot submit job to AWS batch when the compute env of Batch is AWS EKS #5817

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waynewang117 opened this issue Feb 26, 2025 · 0 comments
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@waynewang117
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Bug report

Expected behavior and actual behavior

I configured the AWS EKS as the compute env of AWS batch.
Then I submit a job to AWS batch, I got below error.
com.amazonaws.services.batch.model.ClientException: Container overrides or node overrides should not be set for Batch on EKS jobs.

Steps to reproduce the problem

nextflow.config

process {
executor = ‘awsbatch’
queue = 'xxxxxx'
container = 'job-definition://xxxxxx'
}

nextflow run hello -workdir=s3://xxxxxx

Program output

com.amazonaws.services.batch.model.ClientException: Container overrides or node overrides should not be set for Batch on EKS jobs.

Additional context

I guess this is cased by the hardcode "result.setContainerOverrides(container)" in below file.
https://github.com/nextflow-io/nextflow/blob/master/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy#L794

@waynewang117 waynewang117 changed the title Cannot submit job to AWS batch when the compute env is AWS EKS Cannot submit job to AWS batch when the compute env of Batch is AWS EKS Feb 26, 2025
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