Minor Release - v2.4.0

• Update README

• update nextflow assets

  • update container entrypoint script
    • handle s3 uris as projects
    • sync session cache for resume
    • use logdir and workdir as defined in environment variables
  • update job definition to match container entrypoint script
    • create logdir and workdir environment variables
  • update s3 paths to create / use logdir and workdir
  • update generated config
  • use the new (19.07) config syntax for specifying path to awscli

• update step-functions assets

  • optimize codebuild speed
    • increase size of build instance
  • update container builds
    • add apt-get update
    • increase thread counts
    • handle bam index file staging
    • handle non-standard paired read file names
  • update example workflow
    • use a smaller dataset so that the demo runs faster
  • implement ebs-autoscale on docker datavolume for sfn

• implement two stage deployment

• update aio templates

  • remove deprecated parameters
  • make default values for parameters consistent
  • automatically pick 2 AZs in VPCs
  • make stack exports consistent

• update details to core-environment