Retry ConcatVCF if it fails with SIGPIPE

marcelm · marcelm · commit f36218574810 · 2017-10-19T22:06:33.000+02:00
diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
@@ -58,6 +58,9 @@ process {
 
   $ConcatVCF {
     cpus = 8
+    // For unknown reasons, ConcatVCF sometimes fails with SIGPIPE
+    // (exit code 141). Rerunning the process will usually work.
+    errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}
   }
   $CreateRecalibrationTable {
     cpus = 16

Original file line number	Diff line number	Diff line change
`@@ -58,6 +58,9 @@ process {`
`58`	`58`
`59`	`59`	`$ConcatVCF {`
`60`	`60`	`cpus = 8`
	`61`	`+ // For unknown reasons, ConcatVCF sometimes fails with SIGPIPE`
	`62`	`+ // (exit code 141). Rerunning the process will usually work.`
	`63`	`+ errorStrategy = {task.exitStatus == 141 ? 'retry' : 'terminate'}`
`61`	`64`	`}`
`62`	`65`	`$CreateRecalibrationTable {`
`63`	`66`	`cpus = 16`