From dbb3b3b44b3205fb4c1c034da4d73159b346cf37 Mon Sep 17 00:00:00 2001
From: lquayle88 <drlquayle@gmail.com>
Date: Sat, 1 Oct 2022 07:43:46 +0100
Subject: [PATCH] Reinstated maxRetries and increased memory for
 GATK4_MARKDUPLICATES in sbc_sharc.config for sarek

---
 conf/pipeline/sarek/sbc_sharc.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/pipeline/sarek/sbc_sharc.config b/conf/pipeline/sarek/sbc_sharc.config
index 95b3ee3..4ddf2ba 100644
--- a/conf/pipeline/sarek/sbc_sharc.config
+++ b/conf/pipeline/sarek/sbc_sharc.config
@@ -18,7 +18,7 @@ process {
     // error and retry handling
 
     errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' }
-    maxRetries    = 1
+    maxRetries    = 2
 
 
     // process labels
@@ -75,7 +75,7 @@ process {
     }
 
     withName:'GATK4_MARKDUPLICATES' {
-        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory  = { check_max( 20.GB * task.attempt, 'memory' ) }
     }
 
     withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {