From 30e2450569a4c21048e35374e8958b551d9c4902 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 25 Apr 2020 11:38:07 -0500
Subject: [PATCH] Rearrange scripts
---
workflow/main.nf | 38 ++++++++++++++++++++------------------
1 file changed, 20 insertions(+), 18 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 472e226..d8fae4b 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -99,25 +99,27 @@ process trackStart {
"""
}
-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"}}'
+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 {
--
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