diff --git a/modules/nf-core/cellbender/removebackground/main.nf b/modules/nf-core/cellbender/removebackground/main.nf
index 4cd0d6d3c748..ee0b435a1793 100644
--- a/modules/nf-core/cellbender/removebackground/main.nf
+++ b/modules/nf-core/cellbender/removebackground/main.nf
@@ -30,13 +30,14 @@ process CELLBENDER_REMOVEBACKGROUND {
         prefix = task.ext.prefix ?: "${meta.id}"
         args = task.ext.args ?: ""
         use_gpu = task.ext.use_gpu ? "--cuda" : ""
+        input = task.ext.input ?: "${h5ad}"
         """
         TMPDIR=. cellbender remove-background \
             ${args} \
             --cpu-threads ${task.cpus} \
             --estimator-multiple-cpu \
             ${use_gpu} \
-            --input ${h5ad} \
+            --input ${input} \
             --output ${prefix}.h5
         """