From 57095fe79fce706f2fc9ba9f93d3660fbde400a3 Mon Sep 17 00:00:00 2001
From: "Thiseas C. Lamnidis" <thisseass@gmail.com>
Date: Tue, 3 May 2022 16:12:20 +0200
Subject: [PATCH] Update eva.config

Set max heap size for java jobs in `get_software_versions`.
Limited OpenBLAS threading for python jobs that use numpy/pandas.
---
 conf/pipeline/eager/eva.config | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index b563828..ce0db42 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -191,10 +191,17 @@ process {
    
   withName:get_software_versions {
     cache = false
+    beforeScript = '_JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx256m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
     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:kraken_merge {
+  beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
+}
 
+withName:multiqc {
+  beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1;'
 }
 
 profiles {