From 8ae3cba5e3e5466f6d9f42eadaf62b0911c821e9 Mon Sep 17 00:00:00 2001
From: SPearce <simon.pearce@cruk.manchester.ac.uk>
Date: Mon, 15 Aug 2022 11:35:59 +0100
Subject: [PATCH] Reduce MPILEUP to 5GB

---
 conf/crukmi.config | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/conf/crukmi.config b/conf/crukmi.config
index 3e7383b..f73c252 100644
--- a/conf/crukmi.config
+++ b/conf/crukmi.config
@@ -18,6 +18,10 @@ process {
   beforeScript = 'module load apps/singularity/3.8.0'
   executor = 'pbs'
 
+  errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
+  maxErrors = '-1'
+  maxRetries = 3
+
   withLabel:process_low {
     cpus = { check_max( 1 * task.attempt, 'cpus' ) }
     memory = { check_max( 5.GB * task.attempt, 'memory' ) }
@@ -35,7 +39,7 @@ process {
 
   withName: 'SAMTOOLS_MPILEUP' {
     cpus   = 1
-    memory = { 8.GB * task.attempt }
+    memory = { 5.GB * task.attempt }
   }