diff --git a/modules/nf-core/deseq2/differential/templates/deseq2_differential.R b/modules/nf-core/deseq2/differential/templates/deseq2_differential.R
index 9f1af35b532e..9726aec67baa 100755
--- a/modules/nf-core/deseq2/differential/templates/deseq2_differential.R
+++ b/modules/nf-core/deseq2/differential/templates/deseq2_differential.R
@@ -351,9 +351,7 @@ if ((is_valid_string(opt\$exclude_samples_col)) && (is_valid_string(opt\$exclude
 
 if (is_valid_string(opt\$formula)) {
   message("Using user-specified formula: ", opt\$formula)
-  user_f  <- as.formula(opt\$formula)
-  model_f <- update(user_f, ~ 0 + .)
-  model   <- paste(as.character(model_f), collapse = " ")
+  model  <- opt\$formula
 }  else {
   model <- '~ 0'
 
diff --git a/modules/nf-core/deseq2/differential/tests/main.nf.test.snap b/modules/nf-core/deseq2/differential/tests/main.nf.test.snap
index de6a362d82d6..b661eec86ec1 100644
--- a/modules/nf-core/deseq2/differential/tests/main.nf.test.snap
+++ b/modules/nf-core/deseq2/differential/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                         "formula": "~ genotype * treatment",
                         "comparison": "genotypeWT.treatmentTreated"
                     },
-                    "genotype_WT_KO_treatment_Control_Treated.deseq2.results.tsv:md5,793d90d52dcaa7948be0714a7f2f565d"
+                    "genotype_WT_KO_treatment_Control_Treated.deseq2.results.tsv:md5,5612fc7e92a7a9b497b9198471ed3602"
                 ]
             ],
             [
@@ -51,7 +51,7 @@
                         "formula": "~ genotype * treatment",
                         "comparison": "genotypeWT.treatmentTreated"
                     },
-                    "genotype_WT_KO_treatment_Control_Treated.deseq2.model.txt:md5,1ccfae04123ff7797317d5bbd9080f00"
+                    "genotype_WT_KO_treatment_Control_Treated.deseq2.model.txt:md5,82165b8b24da8f8cffafa457290feeb3"
                 ]
             ],
             [
@@ -61,11 +61,11 @@
             "genotype_WT_KO_treatment_Control_Treated.deseq2.dispersion.pdf",
             "genotype_WT_KO_treatment_Control_Treated.dds.rld.rds"
         ],
+        "timestamp": "2026-03-26T21:10:41.865554487",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:49:04.573809688"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "mouse - contrasts - matrix": {
         "content": [
@@ -190,11 +190,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:54:20.534669297",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:54:20.534669297"
+        }
     },
     "mouse - contrasts - matrix - exclude samples": {
         "content": [
@@ -319,11 +319,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:57:07.846675354",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:57:07.846675354"
+        }
     },
     "mouse - contrasts - matrix - lengths": {
         "content": [
@@ -448,11 +448,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:54:41.568608327",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:54:41.568608327"
+        }
     },
     "mouse - contrasts - matrix - strip spikes": {
         "content": [
@@ -577,11 +577,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:55:44.78705434",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:55:44.78705434"
+        }
     },
     "RNAseq - Feature Counts - formula + limma contrast string - interaction": {
         "content": [
@@ -635,7 +635,7 @@
                         "formula": "~ 0 + genotype",
                         "comparison": "genotypeWT - genotypeKO"
                     },
-                    "genotype_WT_KO.deseq2.model.txt:md5,ac7205ad2d20dc34aedba90032d06629"
+                    "genotype_WT_KO.deseq2.model.txt:md5,227c742304821b46168b1ebf10adfdce"
                 ]
             ],
             [
@@ -645,11 +645,11 @@
             "genotype_WT_KO.deseq2.dispersion.pdf",
             "genotype_WT_KO.dds.rld.rds"
         ],
+        "timestamp": "2026-03-26T21:15:08.277275511",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:51:57.150384623"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "mouse - contrasts - matrix - csv": {
         "content": [
@@ -723,11 +723,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:56:05.923791453",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:56:05.923791453"
+        }
     },
     "mouse - contrasts - matrix - no blocking": {
         "content": [
@@ -852,11 +852,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:55:02.666674563",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:55:02.666674563"
+        }
     },
     "RNAseq - Feature Counts - formula + limma contrast string - shrunken": {
         "content": [
@@ -910,7 +910,7 @@
                         "formula": "~ 0 + genotype",
                         "comparison": "genotypeWT - genotypeKO"
                     },
-                    "genotype_WT_KO.deseq2.model.txt:md5,ac7205ad2d20dc34aedba90032d06629"
+                    "genotype_WT_KO.deseq2.model.txt:md5,227c742304821b46168b1ebf10adfdce"
                 ]
             ],
             [
@@ -920,11 +920,11 @@
             "genotype_WT_KO.deseq2.dispersion.pdf",
             "genotype_WT_KO.dds.rld.rds"
         ],
+        "timestamp": "2026-03-26T21:19:23.811021031",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:53:58.660220114"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     },
     "mouse - contrasts - matrix - subset to contrast": {
         "content": [
@@ -1049,11 +1049,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:56:47.562017144",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:56:47.562017144"
+        }
     },
     "mouse - contrasts - matrix - spikes": {
         "content": [
@@ -1178,11 +1178,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:55:23.654595481",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:55:23.654595481"
+        }
     },
     "mouse - contrasts - matrix - vst nsub": {
         "content": [
@@ -1307,11 +1307,11 @@
             "treatment_mCherry_hND6_.deseq2.dispersion.pdf",
             "treatment_mCherry_hND6_.dds.rld.rds"
         ],
+        "timestamp": "2026-01-20T14:56:26.669994057",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:56:26.669994057"
+        }
     },
     "mouse - contrasts - matrix - stub": {
         "content": [
@@ -1728,10 +1728,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-01-20T14:57:21.703291049",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2026-01-20T14:57:21.703291049"
+        }
     }
 }
\ No newline at end of file