From 400f7a82651a303de25f3c1ff3a7b58fa9b002ec Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 25 Apr 2020 11:34:30 -0500
Subject: [PATCH] Move onError and onComplete scripts outside of handlers
---
workflow/main.nf | 43 ++++++++++++++++++++++---------------------
1 file changed, 22 insertions(+), 21 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 93b24b0..472e226 100755
--- a/workflow/main.nf
+++ b/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
}
--
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