From d69af0f287700e82680a958295d41c3aa231b086 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 6 Apr 2021 16:42:22 +0200
Subject: [PATCH] Merging

---
 conf/pipeline/eager/eva.config | 14 +++++++-------
 conf/pipeline/eager/shh.config |  6 ++++++
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config
index 8850cf1..46fddae 100644
--- a/conf/pipeline/eager/eva.config
+++ b/conf/pipeline/eager/eva.config
@@ -63,19 +63,19 @@ process {
    }
       
   withName: fastqc {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
   withName: adapter_removal {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(12000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(12000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
   withName: dedup {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
   withName: markduplicates {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(8000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(8000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
   withName: malt {
@@ -99,11 +99,11 @@ process {
    }
 
   withName: qualimap {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
   withName: damageprofiler {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
   withName: circularmapper {
@@ -115,7 +115,7 @@ process {
    }
 
   withName: preseq {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
    }
 
 }
diff --git a/conf/pipeline/eager/shh.config b/conf/pipeline/eager/shh.config
index 44d1c3c..5046df0 100644
--- a/conf/pipeline/eager/shh.config
+++ b/conf/pipeline/eager/shh.config
@@ -20,6 +20,12 @@ process {
     queue = { task.memory > 756.GB ? 'supercruncher' : 'long' }
   }
   
+  withName: circulargenerator {
+      cpus = { check_max( 1, 'cpus' ) }
+      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+      time = { check_max( 4.h * task.attempt, 'time' ) }
+  }
+  
   withLabel:'sc_tiny'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 1.GB * task.attempt, 'memory' ) }