diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 9c936c6aa5c4fb7e5c02df24996b32e0f43025db..9579ce10f8c0e426fd5c57ed53f83e2049d1a6e0 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -842,7 +842,7 @@ process countData {
   output:
     path ("*.countTable.csv") into counts
     path ("*.countData.summary") into countsQC
-    path ("assignedReads") into inferMetadata_assignedReads
+    path ("assignedReads.csv") into inferMetadata_assignedReads
 
   script:
     """
@@ -888,7 +888,7 @@ process countData {
 // Extract number of assigned reads metadata into channel
 assignedReadsInfer = Channel.create()
 inferMetadata_assignedReads.splitCsv(sep: ",", header: false).separate(
-  assignedReads
+  assignedReadsInfer
 )
 
 /*