From 56f8f54e2b3bfec40bee103298b559001117d93b Mon Sep 17 00:00:00 2001
From: Johannes Alneberg <alneberg@kth.se>
Date: Mon, 3 Sep 2018 10:18:40 +0200
Subject: [PATCH] 2 threads and 2 cpus for each FastQC process

---
 configuration/uppmax-localhost.config | 1 +
 configuration/uppmax-slurm.config     | 1 +
 main.nf                               | 2 +-
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config
index 0ccef7e880..3536627ff7 100644
--- a/configuration/uppmax-localhost.config
+++ b/configuration/uppmax-localhost.config
@@ -101,6 +101,7 @@ process {
     memory = {params.singleCPUMem * 2 * task.attempt}
   }
   withName:RunFastQC {
+    cpus = 2 // FastQC is only capable of running one thread per fastq file.
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withName:RunFreeBayes {
diff --git a/configuration/uppmax-slurm.config b/configuration/uppmax-slurm.config
index a3ff07a0ca..48005ebb4b 100644
--- a/configuration/uppmax-slurm.config
+++ b/configuration/uppmax-slurm.config
@@ -91,6 +91,7 @@ process {
     queue = 'core'
   }
   withName:RunFastQC {
+    cpus = 2 // FastQC is only capable of running one thread per fastq file.
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
   }
   withName:RunFreeBayes {
diff --git a/main.nf b/main.nf
index 66a0db4e5d..c967555402 100644
--- a/main.nf
+++ b/main.nf
@@ -150,7 +150,7 @@ process RunFastQC {
 
   script:
   """
-  fastqc -q ${fastqFile1} ${fastqFile2}
+  fastqc -t 2 -q ${fastqFile1} ${fastqFile2}
   """
 }