diff --git a/modules/nf-core/scds/main.nf b/modules/nf-core/scds/main.nf
index c195d611229..a9be3157eae 100644
--- a/modules/nf-core/scds/main.nf
+++ b/modules/nf-core/scds/main.nf
@@ -20,10 +20,12 @@ process SCDS {
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
+    if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     template 'scds.R'
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.rds
     touch ${prefix}.csv