diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
index eeea8ccc203..1811d7457ff 100644
--- a/modules/nf-core/cellranger/count/main.nf
+++ b/modules/nf-core/cellranger/count/main.nf
@@ -37,6 +37,8 @@ process CELLRANGER_COUNT {
     mkdir -p "${prefix}/outs/filtered_feature_bc_matrix"
     mkdir -p "${prefix}/outs/raw_feature_bc_matrix"
     echo "$prefix" > ${prefix}/outs/fake_file.txt
+    echo "$prefix" > ${prefix}/outs/filtered_feature_bc_matrix/fake_file.txt
+    echo "$prefix" > ${prefix}/outs/raw_feature_bc_matrix/fake_file.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":