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
         """
 
diff --git a/modules/nf-core/cellbender/removebackground/tests/main.nf.test b/modules/nf-core/cellbender/removebackground/tests/main.nf.test
index c1213509ddaf..187c5f064203 100644
--- a/modules/nf-core/cellbender/removebackground/tests/main.nf.test
+++ b/modules/nf-core/cellbender/removebackground/tests/main.nf.test
@@ -38,6 +38,41 @@ nextflow_process {
             )
         }
     }
+        test("test_cellbender_removebackground mtx") {
+        config './epochs.config'
+        config './mtx.config'
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/10x_mtx/SRR28679756_raw/matrix.mtx.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/10x_mtx/SRR28679756_raw/barcodes.tsv.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/10x_mtx/SRR28679756_raw/features.tsv.gz', checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+        then {
+            assertAll(
+                {assert process.success},
+                {assert snapshot(
+                        process.out.findAll { key, val -> key.startsWith('versions') },
+                        process.out.h5.collect{file(it[1]).name},
+                        process.out.filtered_h5.collect{file(it[1]).name},
+                        process.out.posterior_h5.collect{file(it[1]).name},
+                        process.out.barcodes.collect{file(it[1]).name},
+                        process.out.metrics.collect{file(it[1]).name},
+                        process.out.report.collect{file(it[1]).name},
+                        process.out.pdf.collect{file(it[1]).name},
+                        process.out.log.collect{file(it[1]).name}
+                    ).match()
+                }
+            )
+        }
+    }
 
     test("test_cellbender_removebackground - stub") {
         options '-stub'
diff --git a/modules/nf-core/cellbender/removebackground/tests/main.nf.test.snap b/modules/nf-core/cellbender/removebackground/tests/main.nf.test.snap
index 65d6369856fa..bce31e86691e 100644
--- a/modules/nf-core/cellbender/removebackground/tests/main.nf.test.snap
+++ b/modules/nf-core/cellbender/removebackground/tests/main.nf.test.snap
@@ -41,6 +41,48 @@
             "nextflow": "25.10.4"
         }
     },
+    "test_cellbender_removebackground mtx": {
+        "content": [
+            {
+                "versions_cellbender": [
+                    [
+                        "CELLBENDER_REMOVEBACKGROUND",
+                        "cellbender",
+                        "0.3.2"
+                    ]
+                ]
+            },
+            [
+                "test.h5"
+            ],
+            [
+                "test_filtered.h5"
+            ],
+            [
+                "test_posterior.h5"
+            ],
+            [
+                "test_cell_barcodes.csv"
+            ],
+            [
+                "test_metrics.csv"
+            ],
+            [
+                "test_report.html"
+            ],
+            [
+                "test.pdf"
+            ],
+            [
+                "test.log"
+            ]
+        ],
+        "timestamp": "2026-05-10T13:44:53.496209",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.03.1"
+        }
+    },
     "test_cellbender_removebackground - stub": {
         "content": [
             {
diff --git a/modules/nf-core/cellbender/removebackground/tests/mtx.config b/modules/nf-core/cellbender/removebackground/tests/mtx.config
new file mode 100644
index 000000000000..675b8d0778c0
--- /dev/null
+++ b/modules/nf-core/cellbender/removebackground/tests/mtx.config
@@ -0,0 +1,6 @@
+
+process {
+    withName: CELLBENDER_REMOVEBACKGROUND {
+        ext.input = "." // --input <current-directory> implies that CBRB will read matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz from the current directory.  
+    }
+}