diff --git a/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/main.nf b/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/main.nf
index 82abfdce4dc6..f273f5ab9efb 100644
--- a/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/main.nf
+++ b/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/main.nf
@@ -32,14 +32,12 @@ workflow ORFTABLE_FASTA_GTF_BUILDORFCATALOGUE {
 
     // 1. Normalise each caller's output. The same module is invoked once per
     //    input emission; dispatch happens inside the template based on the
-    //    `caller` val. Append the caller to meta.id so the normaliser's
-    //    default `${meta.id}` prefix yields caller-disambiguated filenames
-    //    (the merger stages multiple BED12s into `beds/*` and needs unique
-    //    names per caller-sample combination).
-    ch_normalise_in = ch_orf_tables.map { meta, table, caller ->
-        [ meta + [ id: "${meta.id}.${caller}" ], table, caller ]
-    }
-    CUSTOM_ORFNORMALISE ( ch_normalise_in, ch_gtf.first() )
+    //    `caller` val, which this subworkflow's own `ext.prefix` config also
+    //    reads directly to disambiguate output filenames per caller (the
+    //    merger stages multiple BED12s into `beds/*` and needs unique names
+    //    per caller-sample combination). meta.id keeps carrying the true
+    //    sample id through to CUSTOM_ORFNORMALISE's sample_id column.
+    CUSTOM_ORFNORMALISE ( ch_orf_tables, ch_gtf.first() )
 
     // 2. Gather all normalised BED12s + sidecar TSVs across callers and
     //    samples into a single cohort-keyed channel. `.collect()` on an
diff --git a/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/nextflow.config b/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/nextflow.config
index 0836c1058b9e..45481f32093d 100644
--- a/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/nextflow.config
+++ b/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/nextflow.config
@@ -1,4 +1,7 @@
 process {
+    withName: '.*ORFTABLE_FASTA_GTF_BUILDORFCATALOGUE:CUSTOM_ORFNORMALISE' {
+        ext.prefix = { "${meta.id}.${caller}.normalised" }
+    }
     withName: '.*ORFTABLE_FASTA_GTF_BUILDORFCATALOGUE:BEDTOOLS_GETFASTA' {
         ext.prefix = { "${meta.id}.catalogue.nt" }
         ext.args   = '-split -s -nameOnly'
diff --git a/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/tests/main.nf.test.snap b/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/tests/main.nf.test.snap
index 39da8cf7d9e6..751f252043ed 100644
--- a/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/tests/main.nf.test.snap
@@ -15,7 +15,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "2": [
@@ -55,7 +55,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "7": [
@@ -87,7 +87,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "consensus_bed12": [
@@ -111,7 +111,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "multiqc": [
@@ -132,11 +132,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-09-06T21:45:07.866746663",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2026-06-26T13:34:49.442717716"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "homo_sapiens [chr20] - ribotish + ribocode - collapse disabled": {
         "content": [
@@ -154,7 +154,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "2": [
@@ -194,7 +194,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "7": [
@@ -226,7 +226,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "consensus_bed12": [
@@ -250,7 +250,7 @@
                         {
                             "id": "cohort"
                         },
-                        "cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
+                        "cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
                     ]
                 ],
                 "multiqc": [
@@ -271,10 +271,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-09-06T21:45:15.573125652",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.8"
-        },
-        "timestamp": "2026-06-26T13:34:56.775003133"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
\ No newline at end of file