---
AWSTemplateFormatVersion: '2010-09-09'
Description: >-
  (WWPS-GLS-WF-NEXTFLOW-AIO) Creates the complete set of resources needed to run
  genomics workflows using Nextflow on AWS Batch


Mappings:
  TagMap:
    default:
      architecture: "genomics-workflows"
      solution: "nextflow"
      tags:
        - Key: "architecture"
          Value: "genomics-workflows"
        - Key: "solution"
          Value: "nextflow"


Metadata:
  AWS::CloudFormation::Interface:
    ParameterGroups:
      - Label:
          default: "VPC"
        Parameters:
          - Namespace
          - VpcId
          - SubnetIds
          - NumberOfSubnets
      - Label:
          default: "Data Storage"
        Parameters:
          - S3DataBucketName
          - ExistingDataBucket
          - CreateEFS
          - ExistingEFS
      - Label:
          default: "AWS Batch"
        Parameters:
          - DefaultCEMinvCpus
          - DefaultCEMaxvCpus
          - PriorityCEMinvCpus
          - PriorityCEMaxvCpus
      - Label:
          default: "Nextflow Resources"
        Parameters:
          - S3NextflowPrefix
          - S3LogsDirPrefix
          - S3WorkDirPrefix
          - NextflowVersion
          - NextflowVersionSpecified

    ParameterLabels:
      Namespace:
        default: Namespace
      VpcId:
        default: VPC ID
      SubnetIds:
        default: VPC Subnet IDs
      NumberOfSubnets:
        default: Number of Subnets
      S3DataBucketName:
        default: S3 Data Bucket Name
      ExistingDataBucket:
        default: Existing Data Bucket?
      CreateEFS:
        default: Create Amazon EFS File System
      ExistingEFS:
        default: Existing Amazon EFS File System.
      DefaultCEMinvCpus:
        default: Default Min vCPU
      DefaultCEMaxvCpus:
        default: Default Max vCPU
      PriorityCEMinvCpus:
        default: High Priority Min vCPU
      PriorityCEMaxvCpus:
        default: High Priority Max vCPU
      S3NextflowPrefix:
        default: S3 Nextflow Prefix
      S3LogsDirPrefix:
        default: S3 Logs Dir Prefix
      S3WorkDirPrefix:
        default: S3 Work Dir Prefix
      NextflowVersion:
        default: Nextflow Version
      NextflowVersionSpecified:
        default: Nextflow Version Specified?
      TemplateRootUrl:
        default: Template Root URL


Parameters:
  Namespace:
    Type: String
    Description: Namespace (e.g. project name) to use to label resources. Between 4-20 letters, digits, and '-', starting with a letter.
    AllowedPattern: "^[a-zA-Z]{1}[a-zA-Z0-9\\-]{3,19}$"
    ConstraintDescription: "Between 4-20 letters, digits, '-', starting with a letter"
    Default: "nextflow"

  VpcId:
    Type: AWS::EC2::VPC::Id
    Description: 'The VPC to create security groups and deploy AWS Batch to. NOTE: Must be the same VPC as the provided subnet IDs.'
  SubnetIds:
    Type: List<AWS::EC2::Subnet::Id>
    Description: 'Subnets you want your batch compute environment to launch in. We recommend private subnets. NOTE: Must be from the VPC provided.'

  S3DataBucketName:
    Description: >-
      A S3 bucket name for storing analysis results
      The bucket name must respect the S3 bucket naming conventions 
      (can contain lowercase letters, numbers, periods and hyphens).
      If left blank a unique bucket name will be generated.

    Type: String
    Default: ""
    AllowedPattern: "((?=^.{3,63}$)(?!^(\\d+\\.)+\\d+$)(^(([a-z0-9]|[a-z0-9][a-z0-9\\-]*[a-z0-9])\\.)*([a-z0-9]|[a-z0-9][a-z0-9\\-]*[a-z0-9])$)|(^.{0}$))"
    ConstraintDescription: "Must respect S3 bucket naming conventions"

  ExistingDataBucket:
    Description: Does this data bucket already exist?
    Type: String
    AllowedValues:
      - "Yes"
      - "No"
    Default: "No"
  CreateEFS:
    Description: Create Amazon EFS File System, eg for shared data. Mounts to each subnet specified.
    Type: String
    AllowedValues:
      - "Yes"
      - "No"
    Default: "No"
  ExistingEFS:
    Description: Specify existing EFS File System, eg for shared data. You should already have EFS Mounts to each subnet specified. If you select to create a new EFS file system, this parameter will be ignored.
    Type: String
    Default: ""
  NumberOfSubnets:
    Type: Number
    Description: Number of subnets to launch into. Should correspond to the length of Subnet Ids
    MinValue: 1
    MaxValue: 6
  DefaultCEMinvCpus:
    Description: The minimum number of CPUs for the default Batch Compute Environment
    Type: Number
    Default: 0
    MinValue: 0
  DefaultCEMaxvCpus:
    Description: The maximum number of CPUs for the default Batch Compute Environment
    Type: Number
    Default: 100
    MinValue: 0
  PriorityCEMinvCpus:
    Description: The minimum number of CPUs for the high-priority Batch Compute Environment
    Type: Number
    Default: 0
    MinValue: 0
  PriorityCEMaxvCpus:
    Description: The maximum number of CPUs for the high-priority Batch Compute Environment
    Type: Number
    Default: 100 
    MinValue: 0
  S3NextflowPrefix:
    Type: String
    Description: >-
      (Optional) Parent folder in the GWFCore bucket for metadata folders.
    Default: _nextflow
  S3LogsDirPrefix:
    Type: String
    Description: >-
      (Optional) Folder in the GWFCore bucket under the {Nextflow Prefix}
      for session cache and logs.
    Default: logs
  S3WorkDirPrefix:
    Type: String
    Description: >-
      (Optional) Folder in the GWFCore bucket under the {Nextflow Prefix}
      that contains workflow intermediate results
    Default: runs
  NextflowVersion:
    Type: String
    Default: latest
    AllowedValues:
      - latest
      - specify ...
    Description: >-
      Version of Nextflow to use. Select "specify ..." to provide a specific version.
  NextflowVersionSpecified:
    Type: String
    Description: >-
      Specific version of Nextflow to use. Must match a released version number - e.g. "20.04.1".
    Default: ""

  ArtifactBucketName:
    Type: String
    Default: aws-genomics-workflows
    Description: >-
      S3 Bucket where distrubution artifacts and additions scripts are stored
  ArtifactBucketPrefix:
    Type: String
    Default: artifacts  # dist: pin_version
    Description: >-
      Prefix in ArtifactBucketName where distribution artifacts and additions scripts are stored

  TemplateRootUrl:
    Type: String
    Description: >-
      Root URL for where nested templates are stored
    Default: https://aws-genomics-workflows.s3.amazonaws.com/templates
    ConstraintDescription: >-
      Must be a valid S3 URL
    AllowedPattern: "https://[a-z0-9-./]{0,}s3([a-z0-9-.]+)*\\.amazonaws\\.com/[a-z0-9-./]{3,}"


Resources:
  GenomicsWorkflowStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL:  !Sub ${TemplateRootUrl}/gwfcore/gwfcore-root.template.yaml
      Parameters:
        Namespace: !Sub ${Namespace}-gwfcore
        VpcId: !Ref VpcId
        SubnetIds: !Join [",", !Ref SubnetIds ]
        S3BucketName: !Ref S3DataBucketName
        ExistingBucket: !Ref ExistingDataBucket
        CreateEFS: !Ref CreateEFS
        ExistingEFS: !Ref ExistingEFS
        NumberOfSubnets: !Ref NumberOfSubnets
        DefaultCEMinvCpus: !Ref DefaultCEMinvCpus
        DefaultCEMaxvCpus: !Ref DefaultCEMaxvCpus
        PriorityCEMinvCpus: !Ref PriorityCEMinvCpus
        PriorityCEMaxvCpus: !Ref PriorityCEMaxvCpus
        ArtifactBucketName: !Ref ArtifactBucketName
        ArtifactBucketPrefix: !Ref ArtifactBucketPrefix
        TemplateRootUrl: !Ref TemplateRootUrl
      Tags: !FindInMap ["TagMap", "default", "tags"]

  NextflowStack:
    Type: AWS::CloudFormation::Stack
    DependsOn: GenomicsWorkflowStack
    Properties:
      TemplateURL:  !Sub ${TemplateRootUrl}/nextflow/nextflow-resources.template.yaml
      Parameters:
        Namespace: !Sub ${Namespace}-nextflow
        GWFCoreNamespace: !Sub "${Namespace}-gwfcore"
        MountEfs: !Ref CreateEFS
        S3NextflowPrefix: !Ref S3NextflowPrefix
        S3LogsDirPrefix: !Ref S3LogsDirPrefix
        S3WorkDirPrefix: !Ref S3WorkDirPrefix
        NextflowVersion: !Ref NextflowVersion
        NextflowVersionSpecified: !Ref NextflowVersionSpecified
        TemplateRootUrl: !Ref TemplateRootUrl
      Tags: !FindInMap ["TagMap", "default", "tags"]


Outputs:
  NextflowContainerImage:
    Value: !GetAtt NextflowStack.Outputs.NextflowContainerImage
    Export:
      Name: !Sub "${Namespace}-NextflowContainerImage"
    
  NextflowJobDefinition:
    Value: !GetAtt NextflowStack.Outputs.NextflowJobDefinition
    Export:
      Name: !Sub "${Namespace}-NextflowJobDefinition"
    Description: >-
      Batch Job Definition that creates a nextflow head node for running workflows
  
  S3NextFlowBucket:
    Value: !GetAtt NextflowStack.Outputs.NextflowBucket
    Export:
      Name: !Sub "${Namespace}-NextflowBucket"
    Description: >-
      S3 Bucket used to store Nextflow metadata (session cache, logs, and intermediate results)
  S3NextflowLogsDir:
    Value: !GetAtt NextflowStack.Outputs.LogsDir
    Export:
      Name: !Sub "${Namespace}-NextflowLogsDir"
    Description: >-
      S3 URI where nextflow session cache and logs are stored.
  S3NextflowWorkDir:
    Value: !GetAtt NextflowStack.Outputs.WorkDir
    Export:
      Name: !Sub "${Namespace}-NextflowWorkDir"
    Description: >-
      S3 URI where workflow intermediate results are stored.
  
  VpcId:
    Description: >-
      The VPC created for your Nextflow stack.
    Value: !Ref VpcId
  S3DataBucket:
    Value: !GetAtt 'GenomicsWorkflowStack.Outputs.S3BucketName'
    Export:
      Name: !Sub "${Namespace}-DataBucket"
    Description: >-
      S3 bucket for storing genomics workflow input and output data
  BatchDefaultQueue:
    Value: !GetAtt 'GenomicsWorkflowStack.Outputs.DefaultJobQueueArn'
    Export:
      Name: !Sub "${Namespace}-DefaultJobQueue"
    Description: >-
      The default AWS Batch job queue for workflow jobs, based on EC2 SPOT instances
  BatchPriorityQueue:
    Value: !GetAtt 'GenomicsWorkflowStack.Outputs.PriorityJobQueueArn'
    Export:
      Name: !Sub "${Namespace}-PriorityJobQueue"
    Description: >-
      AWS Batch job queue for high priority workflow jobs, based on EC2 On-Demand
      instances
...