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 { -- GitLab