AWSTemplateFormatVersion: 2010-09-09
Description: Main stack that nests other stacks required by the solution
Parameters:
  ArtifactBucketName:
    Type: String
    Description: Choose an existing bucket in your account for deployment artifacts
  LambdaArtifactsS3Prefix:
    Type: String
    Description: 'trailing backslash required - Folder name used by the upload script - keep in sync'
    Default: lambdas/
  CodeBuildArtifactsS3Prefix:
    Type: String
    Description: Folder name used by the upload script - keep in sync
    Default: buildspecs
  CfnTemplatesS3Prefix:
    Type: String
    Description: Folder name used by the upload script - keep in sync
    Default: templates
  WorkflowArtifactsS3Prefix:
    Type: String
    Description: Folder name used by the upload script - keep in sync
    Default: workflows
  WorkflowInputsBucketName:
    Type: String
    Description: New bucket created for users to upload inputs. Make it unique by adding accountId and region in the name
  WorkflowOutputsBucketName:
    Type: String
    Description: New bucket created for workflows to write outputs. Make it unique by adding accountId and region in the name
  ReferenceFastaName:
    Type: String
    Default: GRCh38
  ReferenceFastaS3Uri:
    Type: String
    Default: s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta
  WorkflowIntervalS3Path:
    Type: String
    Default: s3://aws-genomics-static-us-east-1/omics-e2e/intervals.tar
  ClinVarVcfS3Path:
    Type: String
    Default: s3://aws-genomics-static-us-east-1/omics-e2e/clinvar.vcf.gz
  DnSnpVcfS3Uri:
    Type: String
    Default: s3://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
  Mills1000GIndelsVcfS3Uri:
    Type: String
    Default: s3://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  KnownIndelsVcfS3Uri:
    Type: String
    Default: s3://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz
  WorkflowDefinitionFilename:
    Type: String
    Description: File name used by the upload script - keep in sync
    Default: gatkbestpractices.wdl.zip
  CurrentReferenceStoreId:
    Type: String 
    Default: 'NONE'
    Description: 'Provide Reference Store ID if exists in current account-region, else leave it NONE'  
  VariantStoreName:
    Type: String
    Default: omicsvariantstore
    Description: Name of the Omics Variant store
  AnnotationStoreName:
    Type: String
    Default: omicsannotationstore
    Description: Name of the Omics Annotation store

Resources:
  CodeBuildStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/code-build-stack.yml
      TimeoutInMinutes: 20
      Parameters:
        ResourcesS3Bucket: !Ref ArtifactBucketName
        LambdasS3Prefix: !Ref LambdaArtifactsS3Prefix
        BuildSpecS3Prefix: !Ref CodeBuildArtifactsS3Prefix
        DockerGenomesInTheCloud: public.ecr.aws/aws-genomics/broadinstitute/genomes-in-the-cloud:2.4.7-1603303710
        DockerGatk: public.ecr.aws/aws-genomics/broadinstitute/gatk:4.1.9.0

  S3ResourcesStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/s3-stack.yml
      TimeoutInMinutes: 5
      Parameters:
        DataInputBucketName: !Ref WorkflowInputsBucketName
        DataOutputBucketName: !Ref WorkflowOutputsBucketName

  OmicsResourcesStack:
    Type: AWS::CloudFormation::Stack
    DependsOn:
      - S3ResourcesStack
      - CodeBuildStack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/omics-resources-stack.yml
      TimeoutInMinutes: 60
      Parameters:
        OmicsResourcesS3Bucket: !Ref ArtifactBucketName
        OmicsCustomResourceLambdaS3Prefix: !Ref LambdaArtifactsS3Prefix
        OmicsWorkflowInputBucketName: !Ref WorkflowInputsBucketName
        OmicsWorkflowOutputBucketName: !Ref WorkflowOutputsBucketName
        ExistingReferenceStoreId: !Ref CurrentReferenceStoreId
        OmicsReferenceFastaUri: !Ref ReferenceFastaS3Uri
        OmicsReferenceName: !Ref ReferenceFastaName
        OmicsWorkflowDefinitionZipS3: !Sub "s3://${ArtifactBucketName}/${WorkflowArtifactsS3Prefix}/${WorkflowDefinitionFilename}"
        ClinvarS3Path: !Ref ClinVarVcfS3Path
        OmicsVariantStoreName: !Ref VariantStoreName
        OmicsAnnotationStoreName: !Ref AnnotationStoreName

  ApplyS3LifecycleStack:
    Type: AWS::CloudFormation::Stack
    DependsOn:
      - S3ResourcesStack
      - CodeBuildStack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/apply-s3-lifecycle-stack.yml
      TimeoutInMinutes: 10
      Parameters:
        LambdaBucketName: !Ref ArtifactBucketName
        LambdaArtifactPrefix: !Ref LambdaArtifactsS3Prefix
        InputsBucketName: !Ref WorkflowInputsBucketName
        OutputsBucketName: !Ref WorkflowOutputsBucketName
  SfnTaskCheckerStack:
    Type: AWS::CloudFormation::Stack
    DependsOn:
      - OmicsResourcesStack
      - CodeBuildStack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/sfn-task-checker-stack.yml
      TimeoutInMinutes: 10
      Parameters:
        OmicsOutputBucket: !Ref WorkflowOutputsBucketName
        LambdaBucketName: !Ref ArtifactBucketName
        LambdaArtifactPrefix: !Ref LambdaArtifactsS3Prefix

  StepFunctionStack:
    Type: AWS::CloudFormation::Stack
    DependsOn:
      - ApplyS3LifecycleStack
      - SfnTaskCheckerStack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/e2e-sfn-stack.yml
      TimeoutInMinutes: 60
      Parameters:
        ReferenceFastaFileS3Uri: !Ref ReferenceFastaS3Uri
        OmicsVariantStoreName: !Ref VariantStoreName
        DbSnpVcf: !Ref DnSnpVcfS3Uri
        Mills1000GIndelsVcf: !Ref Mills1000GIndelsVcfS3Uri
        KnownIndelsVcf: !Ref KnownIndelsVcfS3Uri
        OmicsImportSequenceLambdaArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsImportSequenceLambdaArn
        OmicsImportSequenceJobRoleArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsImportSequenceJobRoleArn
        CheckOmicsTaskLambdaFunctionArn:
          Fn::GetAtt:
            - SfnTaskCheckerStack
            - Outputs.CheckOmicsTaskLambdaFunctionArn
        OmicsWorkflowStartRunLambdaArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsWorkflowStartRunLambdaArn
        OmicsWorkflowStartRunJobRoleArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsWorkflowStartRunJobRoleArn
        OmicsImportVariantLambdaArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsImportVariantLambdaArn
        OmicsImportVariantJobRoleArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsImportVariantJobRoleArn
        ApplyS3LifecycleLambdaFunctionArn:
          Fn::GetAtt: 
            - ApplyS3LifecycleStack
            - Outputs.ApplyS3LifecycleLambdaFunctionArn
  SfnTriggerStack:
    Type: AWS::CloudFormation::Stack
    DependsOn:
      - StepFunctionStack
    Properties:
      TemplateURL: !Sub https://${ArtifactBucketName}.s3.amazonaws.com/${CfnTemplatesS3Prefix}/sfn-trigger-stack.yml
      TimeoutInMinutes: 5
      Parameters:
        FastqInputBucket: !Ref WorkflowInputsBucketName
        GenomicsStepFunctionArn:
          Fn::GetAtt: 
            - StepFunctionStack
            - Outputs.AmazonOmicsStepFunctionArn
        LambdaBucketName: !Ref ArtifactBucketName
        LambdaArtifactPrefix: !Ref LambdaArtifactsS3Prefix
        SequenceStoreId:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsSequenceStoreId
        ReferenceArn:
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsReferenceArn
        WorkflowId: 
          Fn::GetAtt:
            - OmicsResourcesStack
            - Outputs.OmicsWorkflowId
        WorkflowOutputS3Path: !Sub "s3://${WorkflowOutputsBucketName}/outputs"
        GatkDockerUri: 
          Fn::GetAtt:
            - CodeBuildStack
            - Outputs.EcrImageUriGatk
        GotcDockerUri:
          Fn::GetAtt:
            - CodeBuildStack
            - Outputs.EcrImageUriGotc
        IntervalS3Path: !Ref WorkflowIntervalS3Path