diff --git a/modules/nf-core/sambamba/depth/main.nf b/modules/nf-core/sambamba/depth/main.nf
index e1404c7b0dba..42a1a80a323a 100644
--- a/modules/nf-core/sambamba/depth/main.nf
+++ b/modules/nf-core/sambamba/depth/main.nf
@@ -50,7 +50,7 @@ process SAMBAMBA_DEPTH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        sambamba: \$(sambamba --version)
+        sambamba: \$(echo \$(sambamba --version 2>&1) | awk '{print \$2}' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test b/modules/nf-core/sambamba/depth/tests/main.nf.test
index 3f51059861b7..3f6fce50be03 100644
--- a/modules/nf-core/sambamba/depth/tests/main.nf.test
+++ b/modules/nf-core/sambamba/depth/tests/main.nf.test
@@ -30,7 +30,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
             )
         }
     }
@@ -85,7 +88,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    process.out.versions.collect{ path(it).yaml }
+                ).match() }
             )
         }
     }
diff --git a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap
index 7f4951e62acb..d1eb47aaa682 100644
--- a/modules/nf-core/sambamba/depth/tests/main.nf.test.snap
+++ b/modules/nf-core/sambamba/depth/tests/main.nf.test.snap
@@ -29,10 +29,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-03T15:57:58.097957"
+        "timestamp": "2025-12-05T12:03:11.190921915"
     },
     "test-sambamba-depth": {
         "content": [
@@ -61,13 +61,20 @@
                 "versions": [
                     "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57"
                 ]
-            }
+            },
+            [
+                {
+                    "SAMBAMBA_DEPTH": {
+                        "sambamba": "1.0.1"
+                    }
+                }
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-03T15:57:42.031913"
+        "timestamp": "2025-12-05T12:03:07.689091449"
     },
     "test-sambamba-depth-stub": {
         "content": [
@@ -82,7 +89,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce"
+                    "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57"
                 ],
                 "bed": [
                     [
@@ -94,14 +101,21 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,cc89620fa5c4f3af3aebf53eadd3edce"
+                    "versions.yml:md5,6e2f38cc3306b1ea59da275d9de28d57"
                 ]
-            }
+            },
+            [
+                {
+                    "SAMBAMBA_DEPTH": {
+                        "sambamba": "1.0.1"
+                    }
+                }
+            ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-03T15:58:13.647811"
+        "timestamp": "2025-12-05T12:03:14.737096819"
     }
 }
\ No newline at end of file