Move onError and onComplete scripts outside of handlers

workflow/main.nf

@@ -99,31 +99,32 @@ process trackStart {
   """
 }
 
-workflow.onError{
-  errorScript = """singularity run 'docker://bicf/awscli:1.1' \ 
-    aws dynamodb update-item \
-      --table-name pipeline.tracking \
-      --key '{ \
-        "sessionId": {"S": "${workflow.sessionId}"}, \
-        "projectDir": {"S": "${workflow.projectDir}"}}' \
-      --update-expression 'SET #status = :status'  \
-      --expression-attribute-names '{"#status": "status"}' \
-      --expression-attribute-values '{":status": {"S":"error"}}'
+errorScript = """singularity run 'docker://bicf/awscli:1.1' \ 
+  aws dynamodb update-item \
+    --table-name pipeline.tracking \
+    --key '{ \
+      "sessionId": {"S": "${workflow.sessionId}"}, \
+      "projectDir": {"S": "${workflow.projectDir}"}}' \
+    --update-expression 'SET #status = :status'  \
+    --expression-attribute-names '{"#status": "status"}' \
+    --expression-attribute-values '{":status": {"S":"error"}}'
   """
+completeScript = """singularity run 'docker://bicf/awscli:1.1' \ 
+  aws dynamodb update-item \
+    --table-name pipeline.tracking \
+    --key '{ \
+      "sessionId": {"S": "${workflow.sessionId}"}, \
+      "projectDir": {"S": "${workflow.projectDir}"}}' \
+    --update-expression 'SET #status = :status'  \
+    --expression-attribute-names '{"#status": "status"}' \
+    --expression-attribute-values '{":status": {"S":"complete"}}'
+"""
+
+workflow.onError {
   errorResult = errorScript.execute().text
 }
 
-workflow.onComplete{
-  completeScript = """singularity run 'docker://bicf/awscli:1.1' \ 
-    aws dynamodb update-item \
-      --table-name pipeline.tracking \
-      --key '{ \
-        "sessionId": {"S": "${workflow.sessionId}"}, \
-        "projectDir": {"S": "${workflow.projectDir}"}}' \
-      --update-expression 'SET #status = :status'  \
-      --expression-attribute-names '{"#status": "status"}' \
-      --expression-attribute-values '{":status": {"S":"complete"}}'
-  """
+workflow.onComplete {
   completeResult = completeScript.execute().text
 }