From 8b9744723caf27536d42814ce4a150d31faba8f3 Mon Sep 17 00:00:00 2001
From: Emil <raysloks@gmail.com>
Date: Wed, 4 May 2022 14:13:24 +0200
Subject: [PATCH 1/5] Fixes hasta java memory issues

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

diff --git a/conf/hasta.config b/conf/hasta.config
index c5dd5e4..7db9b4c 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -21,6 +21,14 @@ params {
 process {
     executor = 'slurm'
     clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }    
+    
+    withName: QUALIMAP_BAMQC {
+        memory = 64.GB
+        ext.args = "--java-mem-size=60G"
+    }
+    withName: 'PICARD_COLLECTHSMETRICS|PICARD_COLLECTMULTIPLEMETRICS|COLLECTREADCOUNTS|DENOISEREADCOUNTS' {
+        clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}+2" : null }
+    }
 }
 
 profiles {

From e938f3606f012c4bf583a26544236205fae83ed0 Mon Sep 17 00:00:00 2001
From: Emil <raysloks@gmail.com>
Date: Thu, 5 May 2022 14:09:45 +0200
Subject: [PATCH 2/5] Removes the new SGE clusterOptions for now

---
 conf/hasta.config | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/conf/hasta.config b/conf/hasta.config
index 7db9b4c..67d8652 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -26,9 +26,6 @@ process {
         memory = 64.GB
         ext.args = "--java-mem-size=60G"
     }
-    withName: 'PICARD_COLLECTHSMETRICS|PICARD_COLLECTMULTIPLEMETRICS|COLLECTREADCOUNTS|DENOISEREADCOUNTS' {
-        clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}+2" : null }
-    }
 }
 
 profiles {

From 19497a4183123c8694093889ace39fd162ca7b44 Mon Sep 17 00:00:00 2001
From: Emil <raysloks@gmail.com>
Date: Mon, 30 May 2022 11:06:48 +0200
Subject: [PATCH 3/5] Makes qualimap fix work for most memory amounts

---
 conf/hasta.config | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/conf/hasta.config b/conf/hasta.config
index 67d8652..b83f906 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -23,8 +23,7 @@ process {
     clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }    
     
     withName: QUALIMAP_BAMQC {
-        memory = 64.GB
-        ext.args = "--java-mem-size=60G"
+        ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
     }
 }
 

From 29fa08c43439bd277d3ac2fc72826bf0cbc8641a Mon Sep 17 00:00:00 2001
From: Emil <raysloks@gmail.com>
Date: Mon, 30 May 2022 11:07:24 +0200
Subject: [PATCH 4/5] Adds _JAVA_OPTIONS to singularity whitelist

---
 conf/hasta.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conf/hasta.config b/conf/hasta.config
index b83f906..862676a 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -10,6 +10,7 @@ params {
 
 singularity {
   enabled = true
+  envWhitelist = ['_JAVA_OPTIONS']
 }
 
 params {

From 8453f6b41a31146d512694175490b9e478a44a0d Mon Sep 17 00:00:00 2001
From: Emil <raysloks@gmail.com>
Date: Mon, 30 May 2022 12:58:12 +0200
Subject: [PATCH 5/5] Moves qualimap arg to pipeline-specific config

---
 conf/hasta.config                      | 4 ----
 conf/pipeline/raredisease/hasta.config | 3 +++
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/conf/hasta.config b/conf/hasta.config
index 862676a..7e97e5a 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -22,10 +22,6 @@ params {
 process {
     executor = 'slurm'
     clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }    
-    
-    withName: QUALIMAP_BAMQC {
-        ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
-    }
 }
 
 profiles {
diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config
index 96e3332..a076dbc 100644
--- a/conf/pipeline/raredisease/hasta.config
+++ b/conf/pipeline/raredisease/hasta.config
@@ -7,4 +7,7 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
+    withName:'QUALIMAP_BAMQC' {
+        ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
+    }
 }
\ No newline at end of file