Merge pull request #488 from marcelm/concatvcf-resources

Reduce ConcatVCF resources to sane levels
SciLifeLab · Oct 27, 2017 · 0d7fc10 · 0d7fc10
2 parents f79642e + f362185
commit 0d7fc10
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
@@ -57,8 +57,10 @@ process {
   // These processes are defined in main.nf
 
   $ConcatVCF {
-    cpus = 16
-    memory = {params.totalMemory}
+    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