Merge pull request #632 from alneberg/Fastqc_threading

2 threads and 2 cpus for each FastQC process

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 {

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 {

main.nf

@@ -150,7 +150,7 @@ process RunFastQC {
 
   script:
   """
-  fastqc -q ${fastqFile1} ${fastqFile2}
+  fastqc -t 2 -q ${fastqFile1} ${fastqFile2}
   """
 }