Merge pull request #56 from wleepang/update/optional-bucket-name

fix bucket name propagation to nested templates

Author: wleepang

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

@@ -224,7 +224,8 @@ Resources:
         KeyName: !Ref 'KeyPairName'
         SSHLocation: !Ref 'SSHLocation'
         HTTPLocation: !Ref 'HTTPLocation'
-        S3BucketName: !Ref 'S3BucketName'
+        # possibly autogenerated s3 bucket name
+        S3BucketName: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvS3Bucket'
         BatchQueue: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvDefaultJobQueueArn'
       Tags: !FindInMap ["TagMap", "default", "tags"]
 

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

@@ -209,11 +209,13 @@ Resources:
     Properties:
       TemplateURL:  !Sub ${TemplateRootUrl}/nextflow/nextflow-resources.template.yaml
       Parameters:
-        S3DataBucketName: !Ref S3DataBucketName
+        # possibly autogenerated bucket name
+        S3DataBucketName: !GetAtt GenomicsWorkflowStack.Outputs.GenomicsEnvS3Bucket
         S3NextflowBucketName:
           Fn::If:
             - UseOneBucket
-            - !Ref S3DataBucketName
+            # possibly autogenerated bucket name
+            - !GetAtt GenomicsWorkflowStack.Outputs.GenomicsEnvS3Bucket
             - !Ref S3NextflowBucketName
         ExistingBucket: 
           Fn::If:

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

@@ -164,7 +164,8 @@ Resources:
     Properties:
       TemplateURL: !Sub ${TemplateRootUrl}/step-functions/sfn-${StateMachine}.template.yaml
       Parameters:
-        S3BucketName: !Ref 'S3BucketName'
+        # possibly autogenerated s3 bucket name
+        S3BucketName: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvS3Bucket'
         BatchJobQueue: !GetAtt 'GenomicsWorkflowStack.Outputs.GenomicsEnvDefaultJobQueueArn'
       Tags: !FindInMap ["TagMap", "default", "tags"]