From df0429ce9d72ae02c0a319d4e14325707cc7b517 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 14:20:39 +0200
Subject: [PATCH] Replace oracle specific _JAVA_OPTIONS to portable
 JAVA_TOOLS_OPTIONS

---
 conf/pipeline/eager/eva.config | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index f35f1ed..f633bae 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -9,7 +9,7 @@ params {
 // Specific nf-core/eager process configuration
 process {
 
-  beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+  beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
 
   maxRetries = 2
 
@@ -69,17 +69,17 @@ process {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
-   
+
   withName: fastqc_after_clipping {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
-    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
 
   withName: adapter_removal {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
-   
+
   withName: bwa {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" }
   }
@@ -188,19 +188,19 @@ process {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
-   
+
   withName:get_software_versions {
     cache = false
     clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
-    beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
+    beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
-  
+
   withName:eigenstrat_snp_coverage {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
-  }  
-  
+  }
+
   withName:kraken_merge {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
   }
@@ -226,7 +226,7 @@ profiles {
 
     process {
 
-        beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+        beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
 
         maxRetries = 2
 
@@ -279,7 +279,7 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
-        
+
         withName: fastqc_after_clipping {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
@@ -404,7 +404,7 @@ profiles {
 
     process {
 
-        beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+        beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
 
         maxRetries = 2
 
@@ -457,7 +457,7 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
-        
+
         withName: fastqc_after_clipping {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }