diff --git a/application/pipeline-stacks/oncoanalyser/assets/run.sh b/application/pipeline-stacks/oncoanalyser/assets/run.sh
index e32604a..a92a43d 100755
--- a/application/pipeline-stacks/oncoanalyser/assets/run.sh
+++ b/application/pipeline-stacks/oncoanalyser/assets/run.sh
@@ -405,8 +405,9 @@ upload_data() {
   aws s3 sync \
     --no-progress \
     --no-follow-symlinks \
-    --exclude='software/*' \
+    --exclude='.nextflow/*' \
     --exclude='assets/*' \
+    --exclude='software/*' \
     --exclude='work/*' \
     ./ "${output_dir}/"
 }
diff --git a/application/pipeline-stacks/star-align-nf/assets/run.sh b/application/pipeline-stacks/star-align-nf/assets/run.sh
index ace164d..8ce3bbc 100755
--- a/application/pipeline-stacks/star-align-nf/assets/run.sh
+++ b/application/pipeline-stacks/star-align-nf/assets/run.sh
@@ -246,8 +246,9 @@ upload_data() {
   aws s3 sync \
     --no-progress \
     --no-follow-symlinks \
-    --exclude='software/*' \
+    --exclude='.nextflow/*' \
     --exclude='assets/*' \
+    --exclude='software/*' \
     --exclude='work/*' \
     ./ "${output_dir}/"
 }