Optimize Nextflow Workflows on AWS Batch with Mountpoint for Amazon S3

This article explains how to optimize Nextflow workflows on AWS Batch by using Mountpoint for Amazon S3 to stream large reference files directly without staging delays.

• Mountpoint for Amazon S3 provides POSIX-like interface for streaming large objects efficiently
• Eliminates bottlenecks from repeatedly staging large static reference files to EBS
• Genomics England reduced variant annotation pipeline delays using Mountpoint with 500GB+ reference data
• Install Mountpoint client in EC2 launch template User Data section
• Configure Nextflow volume to mount S3 directory as read-only
• Pass Mountpoint paths using val directive, not path directive, in Nextflow processes
• Create custom AMI with pre-installed Mountpoint for faster deployments
• Use --allow-other flag for non-root Docker container access to mounted directory

Mountpoint for Amazon S3 significantly accelerates genomic workflows by streaming reference data directly into processes, eliminating time-consuming file staging operations.