diff --git a/merge.nf b/merge.nf
index 0a4c42da..f416fa07 100644
--- a/merge.nf
+++ b/merge.nf
@@ -185,8 +185,8 @@ workflow {
         it.library_id,
         file("${params.results_dir}/${it.project_id}/${it.sample_id}/${it.library_id}_processed.rds")
       ]}
-      // only include libraries that have been processed through scpca-nf
-      .filter{file(it[2]).exists()}
+      // only include libraries that have been processed through scpca-nf and aren't empty
+      .filter{file(it[2]).exists() && file(it[2]).size() > 0}
       // only one row per library ID, this removes all the duplicates that may be present due to CITE/hashing
       .unique()
       // group tuple by project id: [project_id, [library_id1, library_id2, ...], [sce_file1, sce_file2, ...]]