Mount an S3 bucket to a local folder using Nextflow and AWS Batch

[laurentiush]

Hi,

I am trying to use STAR in Nextflow using AWS Batch and STAR requires a path ( --genomeDir ) where the genome files are stored. My genome files are stored on an S3 bucket and when running directly from an EC2 instance, I can mount the S3 bucket using s3fs.

However, it does not seem possible to use s3fs when running AWS Batch.

Is there a way to 'mount' an S3 bucket to a 'local' mountpoint when using Nextflow with AWS Batch?

Thanks!

[laurentiush]

I found the solution by using a launch template and Mountpoint for S3.