AWSTemplateFormatVersion: "2010-09-09"
Description: >-
  (WWPS-GLS-WF-LT) Creates an EC2 Launch Template for AWS Batch based
  genomics workflows

Mappings:
  ScratchMountPointMap:
    step-functions:
      mountpoint: "/var/lib/docker"
    cromwell:
      mountpoint: "/var/lib/docker"
    nextflow:
      mountpoint: "/var/lib/docker"
  TagMap:
    default:
      architecture: "genomics-workflows"
      solution: "default"
      tags:
        - Key: "architecture"
          Value: "genomics-workflows"
        - Key: "solution"
          Value: "default"
  ECSAdditionsMap:
    step-functions:
      additions: |-
        - stop ecs
        - service docker stop
        - cp -au /var/lib/docker /var/lib/docker.bk
        - rm -rf /var/lib/docker/*
        - cd /opt && wget $artifactRootUrl/get-amazon-ebs-autoscale.sh
        - sh /opt/get-amazon-ebs-autoscale.sh
        - sh /opt/amazon-ebs-autoscale/install.sh $scratchPath /dev/sdc > /var/log/ebs-autoscale-install.log 2>&1
        - sed -i 's+OPTIONS=.*+OPTIONS="--storage-driver btrfs"+g' /etc/sysconfig/docker-storage
        - cp -au /var/lib/docker.bk/* /var/lib/docker
        - cd /opt && wget $artifactRootUrl/aws-ecs-additions.tgz && tar -xzf aws-ecs-additions.tgz
        - sh /opt/ecs-additions/ecs-additions-step-functions.sh
        - service docker start
        - start ecs

    cromwell:
      additions: |-
        - stop ecs
        - service docker stop
        - cp -au /var/lib/docker /var/lib/docker.bk
        - rm -rf /var/lib/docker/*
        - cd /opt && wget $artifactRootUrl/get-amazon-ebs-autoscale.sh
        - sh /opt/get-amazon-ebs-autoscale.sh
        - sh /opt/amazon-ebs-autoscale/install.sh $scratchPath /dev/sdc > /var/log/ebs-autoscale-install.log 2>&1
        - sed -i 's+OPTIONS=.*+OPTIONS="--storage-driver btrfs"+g' /etc/sysconfig/docker-storage
        - cp -au /var/lib/docker.bk/* /var/lib/docker
        - cd /usr/local/bin && curl --retry 5 --retry-connrefused $artifactRootUrl/fetch_and_run.sh" -o "fetch_and_run.sh" && chmod a+x ./fetch_and_run.sh
        - service docker start
        - start ecs

    nextflow:
      additions: |-
        - stop ecs
        - service docker stop
        - cp -au /var/lib/docker /var/lib/docker.bk
        - rm -rf /var/lib/docker/*
        - cd /opt && wget $artifactRootUrl/get-amazon-ebs-autoscale.sh
        - sh /opt/get-amazon-ebs-autoscale.sh
        - sh /opt/amazon-ebs-autoscale/install.sh $scratchPath /dev/sdc > /var/log/ebs-autoscale-install.log 2>&1
        - sed -i 's+OPTIONS=.*+OPTIONS="--storage-driver btrfs"+g' /etc/sysconfig/docker-storage
        - cp -au /var/lib/docker.bk/* /var/lib/docker
        - cd /opt && wget $artifactRootUrl/aws-ecs-additions.tgz && tar -xzf aws-ecs-additions.tgz
        - sh /opt/ecs-additions/ecs-additions-nextflow.sh
        - service docker start
        - start ecs

Parameters:
  LaunchTemplateNamePrefix:
    Type: String
    Default: genomics-workflow
    Description: Name of the launch template. This will be made unique using the Stack ID.
  ScratchVolumeSize:
    Type: Number
    Default: 20
    Description: The initial size of the scratch volume (GB)
  DockerImageAndMetadataVolumeSize:
    Type: Number
    Default: 75
    Description: The size of the volume Docker will use for image and metadata storage (GB)
  WorkflowOrchestrator:
    Type: String
    Description: The workflow orchestration engine you will use
    Default: step-functions
    AllowedValues:
      - step-functions
      - cromwell
      - nextflow
  ArtifactRootUrl:
    Type: String
    Default: https://s3.amazonaws.com/aws-genomics-workflows/artifacts
    Description: >-
      Root URL for where artifacts / additions scripts are stored

Metadata:
  AWS::CloudFormation::Interface:
    ParameterGroups:
      - Label:
          default: "Required"
        Parameters:
          - WorkflowOrchestrator
          - LaunchTemplateNamePrefix
      - Label:
          default: "Optional"
        Parameters:
          - ScratchVolumeSize
          - DockerImageAndMetadataVolumeSize

Resources:
  EC2LaunchTemplate:
    Type: AWS::EC2::LaunchTemplate
    Properties:
      LaunchTemplateName: !Join ["-", [!Ref LaunchTemplateNamePrefix, !Select [2, !Split ["/", !Ref "AWS::StackId" ]]]]
      LaunchTemplateData:
        TagSpecifications:
          - ResourceType: instance
            Tags:
            - Key: architecture
              Value: !FindInMap ["TagMap", "default", "architecture"]
            - Key: solution
              Value: !Ref WorkflowOrchestrator
        BlockDeviceMappings:
          - Ebs:
              DeleteOnTermination: True
              VolumeSize: 50
              VolumeType: gp2
            DeviceName: /dev/xvda
          - Ebs:
              Encrypted: True
              DeleteOnTermination: True
              VolumeSize: !Ref DockerImageAndMetadataVolumeSize
              VolumeType: gp2
            DeviceName: /dev/xvdcz
          - Ebs:
              Encrypted: True
              DeleteOnTermination: True
              VolumeSize: !Ref ScratchVolumeSize
              VolumeType: gp2
            DeviceName: /dev/sdc
        UserData:
          Fn::Base64: !Sub
            - |
              MIME-Version: 1.0
              Content-Type: multipart/mixed; boundary="==BOUNDARY=="

              --==BOUNDARY==
              Content-Type: text/cloud-config; charset="us-ascii"

              packages:
              - jq
              - btrfs-progs
              - sed
              - wget
              - git
              - amazon-ssm-agent
              - unzip

              runcmd:
              - curl -s "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "/tmp/awscliv2.zip"
              - unzip -q /tmp/awscliv2.zip -d /tmp
              - /tmp/aws/install
              - export scratchPath="${ScratchMountPoint}"
              - export artifactRootUrl="${ArtifactRootUrl}"
              - start amazon-ssm-agent

              ${ECSAdditions}

              --==BOUNDARY==--
            - ECSAdditions:
                Fn::FindInMap:
                  - ECSAdditionsMap
                  - !Ref WorkflowOrchestrator
                  - additions
              ScratchMountPoint:
                Fn::FindInMap:
                  - ScratchMountPointMap
                  - !Ref WorkflowOrchestrator
                  - mountpoint

Outputs:
  LaunchTemplateId:
    Description: >-
      EC2 Launch Template ID to use when creating AWS Batch compute environments
      for genomics workflows
    Value: !Ref EC2LaunchTemplate