diff --git a/modules/nf-core/modkit/pileup/main.nf b/modules/nf-core/modkit/pileup/main.nf
index fc4068cc125d..462f8973ef3c 100644
--- a/modules/nf-core/modkit/pileup/main.nf
+++ b/modules/nf-core/modkit/pileup/main.nf
@@ -59,8 +59,9 @@ process MODKIT_PILEUP {
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.bed
-    touch ${prefix}.bedgraph
+    echo $args
+
+    echo | gzip > ${prefix}.bed.gz
     touch ${prefix}.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
index 2011be7c9e03..3f30af70ec00 100644
--- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
@@ -42,7 +42,12 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "1": [
                     [
@@ -56,7 +61,12 @@
                     "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
                 "bedgz": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "log": [
                     [
@@ -73,9 +83,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-11T14:19:04.629490834"
+        "timestamp": "2025-12-19T09:56:52.060201127"
     },
     "[bam, bai], [fasta, fai], [], phased": {
         "content": [
@@ -128,7 +138,12 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "1": [
                     [
@@ -142,7 +157,12 @@
                     "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
                 "bedgz": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "log": [
                     [
@@ -159,9 +179,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-11T14:19:19.17467827"
+        "timestamp": "2025-12-19T09:57:00.458022339"
     },
     "[bam, bai], [fasta, fai], []": {
         "content": [
@@ -292,7 +312,12 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "1": [
                     [
@@ -306,7 +331,12 @@
                     "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
                 "bedgz": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "log": [
                     [
@@ -323,15 +353,20 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-11T14:19:26.675056899"
+        "timestamp": "2025-12-19T09:57:04.868976217"
     },
     "[bam, bai], [], [] - stub": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "1": [
                     [
@@ -345,7 +380,12 @@
                     "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
                 "bedgz": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "log": [
                     [
@@ -362,15 +402,20 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-11T14:18:56.962234621"
+        "timestamp": "2025-12-19T09:56:47.829913052"
     },
     "[bam, bai], [fasta, fai], bed - stub": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "1": [
                     [
@@ -384,7 +429,12 @@
                     "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
                 "bedgz": [
-                    
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "log": [
                     [
@@ -401,8 +451,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-12-11T14:19:11.953321139"
+        "timestamp": "2025-12-19T09:56:56.290093996"
     }
 }
\ No newline at end of file