From 1c942759ea9e30822181fb9d854744f102c62e18 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 18 Aug 2022 15:52:31 +0200
Subject: [PATCH] update sentieon

---
 conf/pipeline/raredisease/hasta.config | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index fb4d94a..1bec159 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -8,7 +8,14 @@ process {
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
     withLabel:'sentieon' {
-        beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202010.02/bin" }
+        beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
+    }
+    // Java memory fixes
+    withName:'QUALIMAP_BAMQC' {
+        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" : ''}" }
     }
     withName: BCFTOOLS_VIEW {
         if (params.genome == 'GRCh37') {