example7

Run nf-core/rnaseq using Conda-based containers and Fusion file system

Summary

This example shows how to run the nf-core/rnaseq pipeline with AWS Batch using Fusion to access the AWS S3 storage and the Wave service to provision the pipeline containers on-demand, by using the Conda recipes defined in the pipeline configuration.

Config

wave {
  enabled = true
  strategy = 'conda,container'
}
 
docker {
  enabled = true
}

fusion {
  enabled = true
  exportStorageCredentials = true
}

Run it

nextflow run nf-core/rnaseq \
	-profile conda,test \
        -work-dir s3://<YOUR BUCKET>/work \
        --outdir s3://<YOUR BUCKET>/results

Note: Make sure to specify an AWS S3 bucket to which you have read-write access as work directory.

AWS credentials to access the bucket should be available either via Environment variables, Amazon ECS container credentials or Instance profile credentials.