---
AWSTemplateFormatVersion: '2010-09-09'
Description: Setup Batch genomics pipeline infrastructure

Parameters:
  TemplatesBucket:
    Description: "S3 bucket that stores the nested templates"
    Type: String
  ImageId:
    Description: "Image ID for BatchGenomics AMI."
    Type: String

Resources:
  # Bucket to store job results
  JobResultsBucket:
    Type: "AWS::S3::Bucket"
  VPCStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub "https://s3.${AWS::Region}.amazonaws.com/${TemplatesBucket}/vpc_template_cfn.yml"
      TimeoutInMinutes: '5'
  RoleStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub "https://s3.${AWS::Region}.amazonaws.com/${TemplatesBucket}/roles_template_cfn.yml"
      TimeoutInMinutes: '5'
  BatchEnvStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub "https://s3.${AWS::Region}.amazonaws.com/${TemplatesBucket}/batch_env_template_cfn.yml"
      Parameters:
        RoleStackName: !GetAtt RoleStack.Outputs.StackName
        VPCStackName: !GetAtt VPCStack.Outputs.StackName
        ImageId: !Sub "${ImageId}"
      TimeoutInMinutes: '5'
  BatchJobStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub "https://s3.${AWS::Region}.amazonaws.com/${TemplatesBucket}/batch_jobs_template_cfn.yml"
      Parameters:
        RoleStackName: !GetAtt RoleStack.Outputs.StackName
        JobResultsBucket: !Ref JobResultsBucket
      TimeoutInMinutes: '5'
  StateMachineStack:
    Type: AWS::CloudFormation::Stack
    Properties:
      TemplateURL: !Sub "https://s3.${AWS::Region}.amazonaws.com/${TemplatesBucket}/state_machine_template_cfn.yml"
      Parameters:
        RoleStackName: !GetAtt RoleStack.Outputs.StackName
      TimeoutInMinutes: '5'

Outputs:
  ImageId:
    Value: !Sub "${ImageId}"
  # Makes job results bucket available to other stacks
  JobResultsBucket:
    Description: JobResultsBucket
    Value: !Ref JobResultsBucket
  # Makes state machine stack name available to other stacks
  StateMachineStack:
    Description: StateMachineStack
    Value: !GetAtt StateMachineStack.Outputs.StackName
  # Generate the example workflow input by adding in the jobs result bucket.
  # This input is used in the run.sh command.
  FullWorkflowInput:
    Description: Full workflow input
    Value: !Sub |-
      {
        "isaac": {
          "WorkingDir": "/scratch",
          "JobName": "isaac1",
          "FastQ1S3Path": "s3://aws-batch-genomics-shared/secondary-analysis/example-files/fastq/SRR1919605_1.fastq.gz",
          "BAMS3FolderPath": "s3://${JobResultsBucket}/NA12878/bam",
          "FastQ2S3Path": "s3://aws-batch-genomics-shared/secondary-analysis/example-files/fastq/SRR1919605_1.fastq.gz",
          "ReferenceS3Path": "s3://aws-batch-genomics-shared/secondary-analysis/reference/isaac/"
        },
        "strelka": {
          "WorkingDir": "/scratch",
          "JobName": "strelka1",
          "BAIS3Path": "s3://${JobResultsBucket}/NA12878/bam/sorted.bam.bai",
          "BAMS3Path": "s3://${JobResultsBucket}/NA12878/bam/sorted.bam",
          "VCFS3Path": "s3://${JobResultsBucket}/NA12878/vcf",
          "ReferenceS3Path": "s3://aws-batch-genomics-shared/secondary-analysis/reference/hg38.fa",
          "ReferenceIndexS3Path": "s3://aws-batch-genomics-shared/secondary-analysis/reference/hg38.fa.fai"
        },
        "samtools": {
          "WorkingDir": "/scratch",
          "JobName": "samtools1",
          "BAMS3Path": "s3://${JobResultsBucket}/NA12878/bam/sorted.bam",
          "ReferenceS3Path": "s3://aws-batch-genomics-shared/secondary-analysis/reference/hg38.fa",
          "BAMStatsS3Path": "s3://${JobResultsBucket}/NA12878/bam/sorted.bam.stats"
        },
        "snpeff": {
          "WorkingDir": "/scratch",
          "JobName": "snpeff1",
          "VCFS3Path": "s3://${JobResultsBucket}/NA12878/vcf/variants/genome.vcf.gz",
          "AnnotatedVCFS3Path": "s3://${JobResultsBucket}/NA12878/vcf/genome.anno.vcf",
          "CommandArgs": " -t hg38 "
        }
      }
  # A minimal example workflow input.  All the job definitions have defaults.
  MinimalWorkflowInput:
    Description: Minimal workflow input
    Value: !Sub |-
      {
        "isaac": {},
        "strelka": {},
        "samtools": {},
        "snpeff": {}
      }

# TEMPLATES_BUCKET=$(aws cloudformation describe-stacks --stack-name batch-genomics-zone --query 'Stacks[].Outputs[?OutputKey==`TemplatesBucket`].OutputValue' --output text)
# IMAGE_ID=$(aws cloudformation describe-stacks --stack-name batch-genomics-pipeline --query 'Stacks[].Outputs[?OutputKey==`ImageId`].OutputValue' --output text)

# aws cloudformation update-stack --stack-name batch-genomics-pipeline --template-body file://template_cfn.yml --capabilities CAPABILITY_NAMED_IAM --output text --parameters ParameterKey=TemplatesBucket,ParameterValue=${TEMPLATES_BUCKET} ParameterKey=ImageId,ParameterValue=${IMAGE_ID};aws cloudformation wait stack-update-complete --stack-name batch-genomics-pipeline

# aws cloudformation create-stack --stack-name batch-genomics-pipeline --template-body file://template_cfn.yml --enable-termination-protection --output text --parameters ParameterKey=TemplatesBucket,ParameterValue=${TEMPLATES_BUCKET} ParameterKey=ImageId,ParameterValue=${IMAGE_ID}; aws cloudformation wait stack-create-complete --stack-name batch-genomics-pipeline