From e5f2a63079f644894a11cb42b3aa16dfd36d40ba Mon Sep 17 00:00:00 2001
From: ameynert <alison.meynert@igmm.ed.ac.uk>
Date: Tue, 30 Mar 2021 16:21:53 +0100
Subject: [PATCH] Java overhead processes list updated

Added all processes calling GATK for Mutect2 variant calling
---
 conf/pipeline/sarek/eddie.config | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/conf/pipeline/sarek/eddie.config b/conf/pipeline/sarek/eddie.config
index 33c4e02..9629337 100644
--- a/conf/pipeline/sarek/eddie.config
+++ b/conf/pipeline/sarek/eddie.config
@@ -30,4 +30,22 @@ process {
   withName:GenotypeGVCFs {
     clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
   }
+  withName:Mutect2 {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:MergeMutect2Stats {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:PileupSummariesForMutect2 {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:MergePileupSummaries {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:CalculateContamination {  
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }
+  withName:FilterMutect2Calls {
+    clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
+  }  
 }