From adfb5366b93c5a03af86c147d369d222add6cc8d Mon Sep 17 00:00:00 2001
From: ameynert <alison.meynert@igmm.ed.ac.uk>
Date: Tue, 30 Mar 2021 16:15:17 +0100
Subject: [PATCH] Java overhead process list updated

Added HaplotypeCaller and GenotypeGVCFs to set of processes that need Java overhead
---
 conf/pipeline/sarek/eddie.config | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/conf/pipeline/sarek/eddie.config b/conf/pipeline/sarek/eddie.config
index 3e1b811..33c4e02 100644
--- a/conf/pipeline/sarek/eddie.config
+++ b/conf/pipeline/sarek/eddie.config
@@ -24,4 +24,10 @@ process {
   withName:GatherBQSRReports {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
+  withName:HaplotypeCaller {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:GenotypeGVCFs {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
 }