Added exit code 140

Author: jfy133

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#673](https://github.com/nf-core/eager/pull/673) Fix Kraken database loading when loading from directory instead of compressed file.
 - [#688](https://github.com/nf-core/eager/issues/668) - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
 - [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex.
+- Added exit code `140` to re-tryable exit code list to account for certain scheduler wall-time limit fails.
 
 ### `Dependencies`
 

conf/base.config

@@ -14,7 +14,7 @@ process {
   memory = { check_max( 7.GB * task.attempt, 'memory' ) }
   time = { check_max( 24.h * task.attempt, 'time' ) }
 
-  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+  errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'retry' : 'finish' }
   maxRetries = 3
   maxErrors = '-1'
 
@@ -74,34 +74,34 @@ process {
   }
 
   withName:qualimap{
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
   }
 
   withName:preseq {
     errorStrategy = 'ignore'
   }
 
   withName:damageprofiler {
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' }
   }
 
   // Add 1 retry for certain java tools as not enough heap space java errors gives exit code 1
   withName: dedup {
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } 
   }
 
   withName: markduplicates {
-    errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [143,137, 140] ? 'retry' : 'finish' } 
   }
 
   // Add 1 retry as not enough heapspace java error gives exit code 1
   withName: malt {
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139, 140] ? 'retry' : 'finish' } 
   }
 
   // other process specific exit statuses
   withName: nuclear_contamination {
-    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'ignore' : 'retry' }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139, 140] ? 'ignore' : 'retry' }
   }
 
 }