From 72e995f32678c8a94c0a466f91b61973363d528b Mon Sep 17 00:00:00 2001
From: Emil Bertilsson <emil.bertilsson@hasta.scilifelab.se>
Date: Thu, 9 Jun 2022 10:28:20 +0200
Subject: [PATCH] Adds generic fix for java memory issue on slurm

---
 conf/pipeline/raredisease/hasta.config | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index a076dbc..c31b940 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -7,7 +7,13 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
+
+    // Java memory fixes
     withName:'QUALIMAP_BAMQC' {
-        ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
     }
+    withName:'PICARD_MARKDUPLICATES' {
+        clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" }
+    }
+    
 }
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