Merge pull request nf-core#632 from alneberg/Fastqc_threading

2 threads and 2 cpus for each FastQC process
UCL-BLIC · Sep 4, 2018 · d094e2b · d094e2b
2 parents f813314 + 3130f6a
commit d094e2b
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Showing 3 changed files with 3 additions and 1 deletion.
diff --git 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
@@ -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
@@ -150,7 +150,7 @@ process RunFastQC {
 
   script:
   """
-  fastqc -q ${fastqFile1} ${fastqFile2}
+  fastqc -t 2 -q ${fastqFile1} ${fastqFile2}
   """
 }