Merge branch 'master' into feat/hasta_update

conf/pipeline/raredisease/hasta.config

@@ -10,7 +10,7 @@ process {
     withLabel:'sentieon' {
         beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" }
     }
-    withName: BCFTOOLS_VIEW {
+    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 "'
         } else if (params.genome == 'GRCh38') {
@@ -20,7 +20,13 @@ process {
             enabled: false,
         ]
     }
+
+    // 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" : ''}" }
     }
+    
 }