diff --git a/modules/local/drop_config_runAE.nf b/modules/local/drop_config_runAE.nf
index 40a270c..da45fc3 100644
--- a/modules/local/drop_config_runAE.nf
+++ b/modules/local/drop_config_runAE.nf
@@ -83,7 +83,9 @@ process DROP_CONFIG_RUN_AE {
     touch OUTRIDER_results_all.Rds
     touch gene_name_mapping_.tsv
     mkdir output
-    mkdir exported_counts
+    if [[ !skip_export_counts_drop ]]; then
+        mkdir exported_counts
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/drop_config_runAS.nf b/modules/local/drop_config_runAS.nf
index 1f04571..c5ea034 100644
--- a/modules/local/drop_config_runAS.nf
+++ b/modules/local/drop_config_runAS.nf
@@ -80,7 +80,9 @@ process DROP_CONFIG_RUN_AS {
     touch FRASER_results_fraser--.tsv
     touch gene_name_mapping_.tsv
     mkdir output
-    mkdir exported_counts
+    if [[ !skip_export_counts_drop ]]; then
+        mkdir exported_counts
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":