Merge pull request #517 from nf-core/jfy133-patch-1

Add base exit codes to try to labelled process settings

Author: jfy133

conf/base.config

@@ -82,22 +82,22 @@ process {
 
   // Add 141 ignore due to unclean pipe closing by pmdtools https://github.com/pontussk/PMDtools/issues/7
   withName: pmdtools {
-    errorStrategy = { task.exitStatus in [141] ? 'ignore' : 'retry' }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139,141] ? 'ignore' : 'retry' }
   }
 
   // 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] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } 
   }
 
   // Add 1 retry as not enough heapspace java error gives exit code 1
   withName: malt {
-    errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139] ? 'retry' : 'finish' } 
   }
 
   // other process specific exit statuses
   withName: nuclear_contamination {
-    errorStrategy = { task.exitStatus in [134] ? 'ignore' : 'retry' }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'ignore' : 'retry' }
   }
 
   withName: multiqc {