AWSTemplateFormatVersion: "2010-09-09"
Description: This template deploys an environment to run Edico Genome's DRAGEN software using AWS Batch. (qs-1oqea6246)

Metadata:
  cfn-lint:
    config:
      ignore_checks:
        - W9006 # temporary to get rid of warnings
        - W9002 # temporary to get rid of warnings
        - W9003 # temporary to get rid of warnings
        - W9901 # Not passing all the default parameters to reduce verbosity
  QuickStartDocumentation:
    EntrypointName: "Parameters for deploying into a new VPC"
    Order: "1"
  AWS::CloudFormation::Interface:
    ParameterGroups:
    - Label:
        default: Network Configuration
      Parameters:
      - AvailabilityZones
      - VPCCIDR
      - PrivateSubnet1CIDR
      - PrivateSubnet2CIDR
      - PublicSubnet1CIDR
      - PublicSubnet2CIDR
    - Label:
        default: DRAGEN Quick Start Configuration
      Parameters:
      - KeyPairName
      - InstanceType
      - BidPercentage
      - MinvCpus
      - MaxvCpus
      - DesiredvCpus
      - GenomicsS3Bucket
      - RetryNumber
    - Label:
        default: AWS Quick Start Configuration
      Parameters:
      - QSS3BucketName
      - QSS3BucketRegion
      - QSS3KeyPrefix
    ParameterLabels:
      AvailabilityZones:
        default: Availability Zones
      KeyPairName:
        default: Key Pair Name
      PrivateSubnet1CIDR:
        default: Private Subnet 1 CIDR
      PrivateSubnet2CIDR:
        default: Private Subnet 2 CIDR
      PublicSubnet1CIDR:
        default: Public Subnet 1 CIDR
      PublicSubnet2CIDR:
        default: Public Subnet 2 CIDR
      VPCCIDR:
        default: VPC CIDR
      QSS3BucketRegion:
        default: Quick Start S3 bucket region
      QSS3KeyPrefix:
        default: Quick Start S3 Key Prefix
      QSS3BucketName:
        default: Quick Start S3 Bucket Name
      InstanceType:
        default: Instance Type
      BidPercentage:
        default: Spot Bid Percentage
      RetryNumber:
        default: AWS Batch Retry Number
      MinvCpus:
        default: Min vCPUs
      MaxvCpus:
        default: Max vCPUs
      DesiredvCpus:
        default: Desired vCPUs
      GenomicsS3Bucket:
        default: Genomics Data Bucket

Parameters:
  AvailabilityZones:
    Description: The list of Availability Zones to use for the subnets in the VPC.
      The Quick Start uses two Availability Zones from your list and preserves the logical order you specify.
    Type: List<AWS::EC2::AvailabilityZone::Name>
  InstanceType:
    AllowedValues:
    - f1.2xlarge
    - f1.4xlarge
    - f1.16xlarge
    Default: f1.4xlarge
    Description: Amazon EC2 instance type for DRAGEN in the AWS Batch Compute Environment.
    Type: String
  KeyPairName:
    Description: The name of an existing public/private key pair, which allows you
      to securely connect to your instance after it launches.
    Type: AWS::EC2::KeyPair::KeyName
  PrivateSubnet1CIDR:
    AllowedPattern: ^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/(1[6-9]|2[0-8]))$
    ConstraintDescription: CIDR block parameter must be in the form x.x.x.x/16-28
    Default: 10.0.0.0/19
    Description: The CIDR block for the private subnet located in Availability Zone 1.
    Type: String
  PrivateSubnet2CIDR:
    AllowedPattern: ^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/(1[6-9]|2[0-8]))$
    ConstraintDescription: CIDR block parameter must be in the form x.x.x.x/16-28
    Default: 10.0.32.0/19
    Description: The CIDR block for the private subnet located in Availability Zone 2.
    Type: String
  PublicSubnet1CIDR:
    AllowedPattern: ^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/(1[6-9]|2[0-8]))$
    ConstraintDescription: CIDR block parameter must be in the form x.x.x.x/16-28
    Default: 10.0.128.0/20
    Description: The CIDR block for the public (DMZ) subnet 1 located in Availability Zone 1.
    Type: String
  PublicSubnet2CIDR:
    AllowedPattern: ^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/(1[6-9]|2[0-8]))$
    ConstraintDescription: CIDR block parameter must be in the form x.x.x.x/16-28
    Default: 10.0.144.0/20
    Description: The CIDR block for the public (DMZ) subnet 2 located in Availability Zone 2.
    Type: String
  VPCCIDR:
    AllowedPattern: ^(([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])\.){3}([0-9]|[1-9][0-9]|1[0-9]{2}|2[0-4][0-9]|25[0-5])(\/(1[6-9]|2[0-8]))$
    ConstraintDescription: CIDR block parameter must be in the form x.x.x.x/16-28
    Default: 10.0.0.0/16
    Description: The CIDR block for the VPC.
    Type: String
  QSS3BucketName:
    AllowedPattern: ^[0-9a-zA-Z]+([0-9a-zA-Z-]*[0-9a-zA-Z])*$
    ConstraintDescription: Quick Start bucket name can include numbers, lowercase
      letters, uppercase letters, and hyphens (-). It cannot start or end with a hyphen
      (-).
    Default: aws-quickstart
    Description: S3 bucket name for the Quick Start assets. Quick Start bucket name
      can include numbers, lowercase letters, uppercase letters, and hyphens (-).
      It cannot start or end with a hyphen (-).
    Type: String
  QSS3BucketRegion:
    Default: 'us-east-1'
    Description: 'The AWS Region where the Quick Start S3 bucket (QSS3BucketName) is hosted. When using your own bucket, you must specify this value.'
    Type: String
  QSS3KeyPrefix:
    AllowedPattern: ^[0-9a-zA-Z-/]*$
    ConstraintDescription: Quick Start key prefix can include numbers, lowercase letters,
      uppercase letters, hyphens (-), and a forward slash (/) at the end of the prefix.
    Description: S3 key prefix for the Quick Start assets. Quick Start key prefix
      can include numbers, lowercase letters, uppercase letters, hyphens (-), and
      forward slash (/).
    Default: quickstart-illumina-dragen/
    Type: String
  BidPercentage:
    AllowedPattern: (?:\b|-)([1-9]{1,2}[0]?|100)\b
    ConstraintDescription: Spot Bid Percentage should be between 1 and 100, inclusive
    Description: The bid percentage set for your AWS Batch Managed Compute Environment with Spot Instances.
    Default: 50
    Type: String
  RetryNumber:
    AllowedPattern: (?:\b|-)([1-9]|10)\b
    ConstraintDescription: AWS Batch job retry number should be between 1 and 10
    Description: Retry number for an AWS Batch job.
    Default: 1
    Type: String
  MinvCpus:
    AllowedPattern: ^(0|[1-9][0-9]{0,2}|1000)$
    ConstraintDescription: Valid between 0 and 1000, inclusive
    Description: Minimum vCPUs for your AWS Batch Compute Environment. Recommend 0.
    Default: 0
    Type: String
  MaxvCpus:
    AllowedPattern: ^([1-9][0-9]{0,2}|1000)$
    ConstraintDescription: Valid between 1 and 1000, inclusive
    Description: Maximum vCPUs for your AWS Batch Compute Environment.
    Type: String
  DesiredvCpus:
    AllowedPattern: ^(0|[1-9][0-9]{0,2}|1000)$
    ConstraintDescription: Valid between 1 and 1000, inclusive
    Description: Desired vCPUs for your AWS Batch Compute Environment. Recommend the same number as MinvCpus for cost-optimization.
    Default: 0
    Type: String
  GenomicsS3Bucket:
    AllowedPattern: ^[0-9a-zA-Z]+([0-9a-zA-Z-]*[0-9a-zA-Z])*$
    ConstraintDescription: S3 genomics bucket name can include numbers, lowercase
      letters, uppercase letters, and hyphens (-). It cannot start or end with a hyphen
      (-).
    Description: S3 bucket name for the bucket to which you'll read and write genomics data. 
    Type: String

Rules:
  DRAGENSupportedRegionRule:
    Assertions:
    - Assert:
        Fn::Contains:
        - - us-east-1
          - us-west-2
          - eu-central-1
          - eu-west-1
          - ap-southeast-2
        - !Ref AWS::Region
      AssertDescription: This Quick Start utilizes DRAGEN Marketplace AMI which is only available
        in specified AWS Regions. Please launch the stack in one of these
        regions to continue.

Conditions:
  UsingDefaultBucket: !Equals [!Ref QSS3BucketName, 'aws-quickstart']

Resources:
  VPCStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL:
        Fn::Sub:
          - https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}submodules/quickstart-aws-vpc/templates/aws-vpc.template.yaml
          - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion]
            S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName]
      Parameters:
        AvailabilityZones:
          Fn::Join:
          - ','
          - !Ref AvailabilityZones
        NumberOfAZs: '2'
        PrivateSubnet1ACIDR: !Ref PrivateSubnet1CIDR
        PrivateSubnet2ACIDR: !Ref PrivateSubnet2CIDR
        PublicSubnet1CIDR: !Ref PublicSubnet1CIDR
        PublicSubnet2CIDR: !Ref PublicSubnet2CIDR
        VPCCIDR: !Ref VPCCIDR
  DragenStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub
        - https://${S3Bucket}.s3.${S3Region}.${AWS::URLSuffix}/${QSS3KeyPrefix}templates/dragen.template.yaml
        - S3Region: !If [UsingDefaultBucket, !Ref 'AWS::Region', !Ref QSS3BucketRegion]
          S3Bucket: !If [UsingDefaultBucket, !Sub '${QSS3BucketName}-${AWS::Region}', !Ref QSS3BucketName]
      Parameters:
        PrivateSubnet1ID: !GetAtt VPCStack.Outputs.PrivateSubnet1AID
        PrivateSubnet2ID: !GetAtt VPCStack.Outputs.PrivateSubnet2AID
        VPCID: !GetAtt VPCStack.Outputs.VPCID
        QSS3BucketName: !Ref QSS3BucketName
        QSS3BucketRegion: !Ref QSS3BucketRegion
        QSS3KeyPrefix: !Ref QSS3KeyPrefix
        KeyPairName: !Ref KeyPairName
        InstanceType: !Ref InstanceType
        BidPercentage: !Ref BidPercentage
        MinvCpus: !Ref MinvCpus
        MaxvCpus: !Ref MaxvCpus
        DesiredvCpus: !Ref DesiredvCpus
        GenomicsS3Bucket: !Ref GenomicsS3Bucket
        RetryNumber: !Ref RetryNumber

Outputs:
  DragenJobDefinition:
    Value: !GetAtt DragenStack.Outputs.DragenJobDefinition
  JobQueue:
    Value: !GetAtt DragenStack.Outputs.JobQueue
  DragenComputeEnvironmentSpot:
    Value: !GetAtt DragenStack.Outputs.DragenComputeEnvironmentSpot
  DragenComputeEnvironmentOnDemand:
    Value: !GetAtt DragenStack.Outputs.DragenComputeEnvironmentOnDemand