Merge pull request #353 from BrunoGrandePhD/patch-1

Retry tasks with exit code 247 for added memory
nf-core · Feb 24, 2021 · f365b81 · f365b81
2 parents 13def96 + 68ca38b
commit f365b81
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [#353](https://github.com/nf-core/sarek/pull/353) - Add support for task retries with exit code 247 (exhibited by Picard MarkDuplicates)
+
 ### Changed
 
 - [#333](https://github.com/nf-core/sarek/pull/333) - Bump `Sarek` version to `3.0dev`

diff --git a/conf/base.config b/conf/base.config
@@ -15,7 +15,7 @@ process {
   time = {check_resource(24.h * task.attempt)}
   shell = ['/bin/bash', '-euo', 'pipefail']
 
-  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+  errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }
   maxErrors = '-1'
   maxRetries = 3