Nextflow AWS Batch Squared

[mehalter]

This repository moves our Nextflow pipeline execution to running entirely in AWS Batch. Where nextflow pipelines are submitted to a workflow queue which in turn spins up more AWS Batch jobs in a job queue for each individual step. This moves us to being able to see when pipelines are running and when they finish as well as avoiding the need to have a Nextflow EC2 instance always running waiting to receive job requests.

Implemented

• New workflows AWS Batch job queue for submitting Nextflow workflows
• Creates an ECR container repository for each swimlane to maintain container images
• Creates a Docker image that installs nextflow and dependencies to execute pipelines

TODO in a followup PR

(need to merge for timeliness sake and pass off deployment rights)

• Create an AWS Batch Job Definition for kicking off Bactopia runs