From dd63dee7aa6422354311dcf4a55945ad18d01f1d Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 18 Aug 2022 15:56:41 +0200
Subject: [PATCH] update conf

---
 conf/pipeline/raredisease/hasta.config | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 1bec159..d655bf7 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -10,13 +10,6 @@ process {
     withLabel:'sentieon' {
         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') {
             ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "'