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wleepangwleepang
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Merge pull request #63 from wleepang/master
update aio templates
2 parents 90e90d7 + 82cd60f commit 4304e11

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‎src/templates/aws-genomics-s3.template.yaml‎

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@@ -60,8 +60,6 @@ Resources:
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- ServerSideEncryptionByDefault:
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SSEAlgorithm: AES256
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Tags:
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- Key: Name
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Value: genomics-base-ami
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- Key: architecture
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Value: !FindInMap ["TagMap", "default", "architecture"]
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‎src/templates/cromwell/cromwell-aio.template.yaml‎

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@@ -1,3 +1,4 @@
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---
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AWSTemplateFormatVersion: "2010-09-09"
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Description: >-
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(WWPS-GLS-WF-CROMWELL-AIO) Creates the complete set of resources needed to run
@@ -20,11 +21,13 @@ Metadata:
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ParameterGroups:
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- Label:
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default: "Required"
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Parameters:
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- KeyPairName
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- Label:
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default: "Data Storage"
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Parameters:
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- S3BucketName
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- ExistingBucket
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- KeyPairName
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- AvailabilityZones
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- Label:
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default: "AWS Batch"
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Parameters:
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# Parameters
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Parameters:
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AvailabilityZones:
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Description: "Choose the two Availability Zones to deploy instances for AWS Batch."
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Type: List<AWS::EC2::AvailabilityZone::Name>
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S3BucketName:
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Description: >-
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A S3 bucket name for storing analysis results.
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- No
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Default: No
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KeyPairName:
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Description: Key Pair name
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Description: Key Pair name used for SSH access to the Cromwell Server.
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Type: AWS::EC2::KeyPair::KeyName
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SpotBidPercentage:
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Description: The percent of on-demand pricing for max bid for Spot intances
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ArtifactRootUrl:
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Type: String
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Default: https://aws-genomics-workflows.s3.amazonaws.com/artifacts
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Default: https://s3.amazonaws.com/aws-genomics-workflows/artifacts
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Description: >-
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Root URL for where artifacts / additions scripts are stored
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@@ -185,9 +185,12 @@ Resources:
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TemplateURL: https://aws-quickstart.s3.amazonaws.com/quickstart-aws-vpc/templates/aws-vpc.template
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TimeoutInMinutes: 15
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Parameters:
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AvailabilityZones: !Join ["," , !Ref AvailabilityZones]
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AvailabilityZones:
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Fn::Join:
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- ","
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- - !Sub "${AWS::Region}a"
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- !Sub "${AWS::Region}b"
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NumberOfAZs: "2"
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KeyPairName: !Ref KeyPairName
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Tags: !FindInMap ["TagMap", "default", "tags"]
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GenomicsWorkflowStack:
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SubnetIds: !Sub "${VpcStack.Outputs.PrivateSubnet1AID}, ${VpcStack.Outputs.PrivateSubnet2AID}"
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S3BucketName: !Ref S3BucketName
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ExistingBucket: !Ref ExistingBucket
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KeyPairName: !Ref 'KeyPairName'
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WorkflowOrchestrator: cromwell
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SpotBidPercentage: !Ref 'SpotBidPercentage'
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DefaultCEMinvCpus: !Ref 'DefaultCEMinvCpus'
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Outputs:
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CromwellServerHostName:
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Value: !GetAtt 'CromwellServerStack.Outputs.HostName'
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Export:
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Name: !Sub "${AWS::StackName}-CromwellServerHostName"
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Description: >-
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Cromwell server public DNS name. Use this URL in a web browser or via curl
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to access Cromwell and submit workflows.
@@ -251,14 +255,21 @@ Outputs:
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Value: !GetAtt 'VpcStack.Outputs.VPCID'
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S3Bucket:
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Value: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvS3Bucket'
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Export:
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Name: !Sub "${AWS::StackName}-S3Bucket"
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Description: >-
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S3 bucket for storing genomics workflow input and output data
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BatchDefaultQueue:
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Value: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvDefaultJobQueueArn'
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Export:
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Name: !Sub "${AWS::StackName}-DefaultJobQueue"
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Description: >-
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The default AWS Batch job queue for workflow jobs, based on EC2 SPOT instances
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BatchHighPriorityQueue:
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Value: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvHighPriorityJobQueueArn'
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Export:
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Name: !Sub "${AWS::StackName}-HighPriorityJobQueue"
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Description: >-
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AWS Batch job queue for high priority workflow jobs, based on EC2 On-Demand
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instances
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...

‎src/templates/nextflow/nextflow-aio.template.yaml‎

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@@ -21,7 +21,7 @@ Metadata:
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AWS::CloudFormation::Interface:
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ParameterGroups:
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- Label:
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default: "Required"
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default: "Data Storage"
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Parameters:
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- S3DataBucketName
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- ExistingDataBucket
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Type: String
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Description: >-
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Root URL for where nested templates are stored
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Default: https://s3.amazonaws.com/pwyming-demo-templates/nextflow-workshop
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Default: https://s3.amazonaws.com/aws-genomics-workflows/templates
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ConstraintDescription: >-
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Must be a valid S3 URL
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AllowedPattern: "https://s3(-[a-z0-9]+)*\\.amazonaws\\.com/[a-z0-9-./]{3,}"
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Outputs:
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NextflowContainerImage:
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Value: !GetAtt NextflowStack.Outputs.NextflowContainerImage
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Export:
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Name: !Sub "${AWS::StackName}-NextflowJobDefinition"
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NextflowJobDefinition:
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Value: !GetAtt NextflowStack.Outputs.NextflowJobDefinition
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Name: !Sub "${AWS::StackName}-HighPriorityJobQueue"
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Description: >-
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AWS Batch job queue for high priority workflow jobs, based on EC2 On-Demand
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instances
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instances
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...

‎src/templates/step-functions/sfn-aio.template.yaml‎

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@@ -19,12 +19,10 @@ Metadata:
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AWS::CloudFormation::Interface:
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ParameterGroups:
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- Label:
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default: "Required"
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default: "Data Storage"
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Parameters:
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- S3BucketName
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- ExistingBucket
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- KeyPairName
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- AvailabilityZones
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- Label:
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default: "AWS Batch"
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Parameters:
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default: S3 Bucket Name
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ExistingBucket:
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default: Existing Bucket?
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KeyPairName:
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default: EC2 Key Pair Name
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SpotBidPercentage:
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default: Spot Bid %
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DefaultCEMinvCpus:
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# Parameters
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Parameters:
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AvailabilityZones:
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Description: "Choose the two Availability Zones to deploy instances for AWS Batch."
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Type: List<AWS::EC2::AvailabilityZone::Name>
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S3BucketName:
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Description: >-
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A S3 bucket name for storing analysis results.
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- Yes
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- No
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Default: No
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KeyPairName:
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Description: Key Pair name
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Type: AWS::EC2::KeyPair::KeyName
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SpotBidPercentage:
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Description: The percent of on-demand pricing for max bid for Spot intances
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Type: Number
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ArtifactRootUrl:
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Type: String
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Default: https://aws-genomics-workflows.s3.amazonaws.com/artifacts
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Default: https://s3.amazonaws.com/aws-genomics-workflows/artifacts
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Description: >-
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Root URL for where artifacts / additions scripts are stored
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@@ -134,9 +124,12 @@ Resources:
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TemplateURL: https://aws-quickstart.s3.amazonaws.com/quickstart-aws-vpc/templates/aws-vpc.template
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TimeoutInMinutes: 15
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Parameters:
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AvailabilityZones: !Join ["," , !Ref AvailabilityZones]
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AvailabilityZones:
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Fn::Join:
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- ","
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- - !Sub "${AWS::Region}a"
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- !Sub "${AWS::Region}b"
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NumberOfAZs: "2"
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KeyPairName: !Ref KeyPairName
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Tags: !FindInMap ["TagMap", "default", "tags"]
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GenomicsWorkflowStack:
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SubnetIds: !Sub "${VpcStack.Outputs.PrivateSubnet1AID}, ${VpcStack.Outputs.PrivateSubnet2AID}"
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S3BucketName: !Ref S3BucketName
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ExistingBucket: !Ref ExistingBucket
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KeyPairName: !Ref 'KeyPairName'
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WorkflowOrchestrator: step-functions
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SpotBidPercentage: !Ref 'SpotBidPercentage'
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DefaultCEMinvCpus: !Ref 'DefaultCEMinvCpus'
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Outputs:
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StateMachine:
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Value: !GetAtt 'SfnStack.Outputs.StateMachine'
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Export:
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Name: !Sub ${AWS::StackName}-StateMachine
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Description: >-
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Example AWS Step Functions state machine
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StateMachineInput:
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Value: !GetAtt 'SfnStack.Outputs.StateMachineInput'
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Description: >-
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Example input for the state machine. Use this when executing your workflow.
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VpcId:
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Description: >-
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The VPC created for your Nextflow stack.
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Value: !GetAtt 'VpcStack.Outputs.VPCID'
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S3Bucket:
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Value: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvS3Bucket'
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Export:
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Name: !Sub ${AWS::StackName}-S3Bucket
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Description: >-
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S3 bucket for storing genomics workflow input and output data
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BatchDefaultQueue:
187187
Value: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvDefaultJobQueueArn'
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Export:
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Name: !Sub ${AWS::StackName}-DefaultJobQueue
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Description: >-
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The default AWS Batch job queue for workflow jobs, based on EC2 SPOT instances
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BatchHighPriorityQueue:
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Value: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvHighPriorityJobQueueArn'
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Export:
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Name: !Sub ${AWS::StackName}-HighPrioirityJobQueue
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Description: >-
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AWS Batch job queue for high priority workflow jobs, based on EC2 On-Demand
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instances

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