diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf
index 1efda00abb8..841ea2fea6c 100644
--- a/modules/nf-core/kallistobustools/count/main.nf
+++ b/modules/nf-core/kallistobustools/count/main.nf
@@ -17,11 +17,9 @@ process KALLISTOBUSTOOLS_COUNT {
     val   workflow_mode
 
     output:
-    tuple val(meta), path ("*.count")                  , emit: count
-    tuple val(meta), path ("*.count/counts_unfiltered"), emit: raw_counts
-    tuple val(meta), path ("*.count/counts_filtered")  , emit: filtered_counts, optional: true
-    path "versions.yml"                                , emit: versions
-    path "*.count/*/*.mtx"                             , emit: matrix //Ensure that kallisto finished and produced outputs
+    tuple val(meta), path ("*.count")   , emit: count
+    path "versions.yml"                 , emit: versions
+    path "*.count/*/*.mtx"              , emit: matrix //Ensure that kallisto finished and produced outputs
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml
index d491dffaae3..55d5dc6cdc4 100644
--- a/modules/nf-core/kallistobustools/count/meta.yml
+++ b/modules/nf-core/kallistobustools/count/meta.yml
@@ -58,14 +58,6 @@ output:
       type: file
       description: kb count output folder
       pattern: "*.{count}"
-  - raw_counts:
-      type: file
-      description: kb raw counts output folder
-      pattern: "*.{count}/counts_unfiltered"
-  - filtered_counts:
-      type: file
-      description: kb filtered counts output folder
-      pattern: "*.{count}/counts_filtered"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
index 6f6b3183328..3378c3c16fa 100644
--- a/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
+++ b/modules/nf-core/kallistobustools/count/tests/main.nf.test.snap
@@ -15,22 +15,9 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
                     "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
                 ],
-                "4": [
+                "2": [
                     "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "count": [
@@ -44,23 +31,10 @@
                             ]
                         ]
                     ]
-                ],
-                "filtered_counts": [
-                    
                 ],
                 "matrix": [
                     "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
-                "raw_counts": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        [
-                            "cells_x_genes.mtx:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
                 "versions": [
                     "versions.yml:md5,6ec06270afe0a7572c41567160d927d9"
                 ]
@@ -70,7 +44,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T11:38:48.980939376"
+        "timestamp": "2024-03-01T15:48:45.775904562"
     },
     "genome.fasta + genome.gtf + '10X3' + 'standard'": {
         "content": [