diff --git a/rna-seq.nf b/rna-seq.nf
index 9765d7bfc112f2bb04a1493378c1feb6d040b5bb..d877bfb9f35d53fb52c0dcece6cf0f26bb70cd02 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -275,7 +275,7 @@ process getData {
     sh ${script_bdbagFetch} \${replicate::-13} ${repRID}
     echo -e "LOG: fetched" >> ${repRID}.getData.log
     
-    fastqCount=\$(ls *.fastq.gz | wc -l)
+    fastqCount=\$(find . -name *.fastq.gz | wc -l)
     if [ "\${fastqCount}" == "0" ]
     then
       touch dummy.R1.fastq.gz