diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
index bca584f43e1b..b48c851b0b9d 100644
--- a/modules/nf-core/seqkit/replace/main.nf
+++ b/modules/nf-core/seqkit/replace/main.nf
@@ -8,7 +8,7 @@ process SEQKIT_REPLACE {
         : 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"
 
     input:
-    tuple val(meta), path(fastx)
+    tuple val(meta), path(fastx, stageAs: "raw.fasta")
 
     output:
     tuple val(meta), path("*.fast*"), emit: fastx
@@ -34,8 +34,8 @@ process SEQKIT_REPLACE {
         replace \\
         ${args} \\
         --threads ${task.cpus} \\
-        -i ${fastx} \\
-        -o ${prefix}.${endswith}
+        -o ${prefix}.${endswith} \\
+        ${fastx}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
index 62bcecd522d6..e0d804dc8761 100644
--- a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
@@ -106,7 +106,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
+                        "test.fasta:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
                     ]
                 ],
                 "1": [
@@ -117,7 +117,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
+                        "test.fasta:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
                     ]
                 ],
                 "versions": [
@@ -126,9 +126,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-01-23T11:36:24.47433864"
+        "timestamp": "2026-01-19T15:03:41.478257363"
     }
 }
\ No newline at end of file