From 92648c1c1fe6a755e1d991e91ccb313f5c26a03c Mon Sep 17 00:00:00 2001
From: "Thiseas C. Lamnidis" <thisseass@gmail.com>
Date: Tue, 12 Oct 2021 15:12:49 +0200
Subject: [PATCH 1/2] added 1240k profile

---
 conf/pipeline/eager/eva.config | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index cf9a9ea..9d2a7e1 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -472,4 +472,34 @@ profiles {
       bwaalnl = 16500
      }
   }
+  1240k {
+    params {
+      // Specific nf-core/configs params
+      config_profile_contact = 'James Fellows Yates (@jfy133)'
+      config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
+    }
+  
+    executor {
+      queueSize = 6
+     }
+
+    process {
+
+      beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
+
+      maxRetries = 2
+
+      // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
+      clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
+
+      // Increasing walltime for bwa to avoid unnecessary retries
+      withName:bwa {
+        time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 72.h : 48.h }
+      }
+    
+      withName:markduplicates {
+        memory = { task.attempt == 3 ? 16.GB : task.attempt == 2 ? 8.GB : 4.GB }
+      }
+    }
+  }
 }

From e741ecb7a7daad939164ed85c0f384feff70af56 Mon Sep 17 00:00:00 2001
From: "Thiseas C. Lamnidis" <thisseass@gmail.com>
Date: Wed, 13 Oct 2021 13:04:41 +0200
Subject: [PATCH 2/2] Update eva.config

---
 conf/pipeline/eager/eva.config | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index 9d2a7e1..5f0eaae 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -475,8 +475,8 @@ profiles {
   1240k {
     params {
       // Specific nf-core/configs params
-      config_profile_contact = 'James Fellows Yates (@jfy133)'
-      config_profile_description = 'nf-core/eager big-data EVA profile provided by nf-core/configs'
+      config_profile_contact = 'Thiseas C. Lamnidis (@TCLamnidis)'
+      config_profile_description = 'nf-core/eager 1240k data EVA profile provided by nf-core/configs'
     }
   
     executor {
@@ -484,14 +484,6 @@ profiles {
      }
 
     process {
-
-      beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"'
-
-      maxRetries = 2
-
-      // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
-      clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
-
       // Increasing walltime for bwa to avoid unnecessary retries
       withName:bwa {
         time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 72.h : 48.h }