diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index b1cf47e81a40efc33376f3e7041d0a5b981e5ed4..07d994f3c14eb61fe0e99c8c3489bb9bd0a5c526 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -914,7 +914,7 @@ process fastqc {
     fastqc *.fastq.gz -o .
 
     # count raw reads
-    zcat ${fastq[0]} | echo $((`wc -l`/4)) > rawReads.csv
+    zcat *.R1.fastq.gz | echo $((`wc -l`/4)) > rawReads.csv
     """
 }