From e2773496886c56d6cf8c4ce2a34c372d0ed34b6e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 8 Jan 2021 09:21:56 -0600
Subject: [PATCH] Add 1 retry to all processes
---
workflow/conf/biohpc.config | 22 ++--------------------
1 file changed, 2 insertions(+), 20 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index e2d47d2..d2323f3 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -6,27 +6,23 @@ process {
executor = 'slurm'
queue = 'super'
clusterOptions = '--hold'
+ errorStrategy = 'retry'
+ maxRetries = 1
withName:trackStart {
executor = 'local'
}
withName:getBag {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:getData {
queue = 'super'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:parseMetadata {
executor = 'local'
}
withName:trimData {
queue = 'super'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:getRefInfer {
queue = 'super'
@@ -69,44 +65,30 @@ process {
}
withName:uploadInputBag {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:uploadExecutionRun {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:uploadQC {
executor = 'local'
}
withName:uploadProcessedFile {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:uploadOutputBag {
executor = 'local'
}
withName:finalizeExecutionRun {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:failPreExecutionRun {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:failPreExecutionRun {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
withName:failExecutionRun {
executor = 'local'
- errorStrategy = 'retry'
- maxRetries = 1
}
}
--
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