diff --git a/workflow/conf/aws_ondemand.config b/workflow/conf/aws_ondemand.config
index 7de0cafc3b9532654b359869f45cd3297655e237..52043ab4da33c04a110605866acb3bc5eba750c2 100755
--- a/workflow/conf/aws_ondemand.config
+++ b/workflow/conf/aws_ondemand.config
@@ -13,6 +13,9 @@ process {
   cpus = 1
   memory = '1 GB'
 
+  withName:getRef {
+    cpus = 8
+  }
   withName:trimData {
     cpus = 15
   }
diff --git a/workflow/conf/aws_spot.config b/workflow/conf/aws_spot.config
index bbf9725ab6158e2540263f40f77db72e53965e77..189ab7e02f21440583feb13606964ab67e7a4f78 100755
--- a/workflow/conf/aws_spot.config
+++ b/workflow/conf/aws_spot.config
@@ -13,6 +13,9 @@ process {
   cpus = 1
   memory = '1 GB'
 
+  withName:getRef {
+    cpus = 8
+  }
   withName:trimData {
     cpus = 15
   }
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index 4797610f870f8e8f22024e0198dc0255c0829073..3667387fbfe89ad88425d2dcbc163b499786f2c7 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -55,9 +55,9 @@ def main():
     # Get strandedness metadata from 'Experiment Settings.csv'
     if (args.parameter == "stranded"):
         if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
-            if endsManual == "se":
+            if (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 1):
                 stranded = "--rna-strandness F"
-            else:
+            elif (len(metaFile[metaFile["File_Type"] == "FastQ"]) == 2):
                 stranded = "--rna-strandness FR"
         elif (metaFile.Has_Strand_Specific_Information.unique() == "no"):
             stranded = ""