diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
index 18a1b99f6e4e..17a05c72d129 100644
--- a/modules/nf-core/seqkit/replace/main.nf
+++ b/modules/nf-core/seqkit/replace/main.nf
@@ -20,7 +20,7 @@ process SEQKIT_REPLACE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}_replaced"
     def extension = "fastq"
     if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.faa|.+\.faa.gz/) {
         extension = "fasta"
@@ -35,7 +35,7 @@ process SEQKIT_REPLACE {
         replace \\
         ${args} \\
         --threads ${task.cpus} \\
-        -i ${fastx} \\
+        ${fastx} \\
         -o ${prefix}.${endswith}
     """
 
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 02bace12eed2..a569fa2959c8 100644
--- a/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
+++ b/modules/nf-core/seqkit/replace/tests/main.nf.test.snap
@@ -33,7 +33,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta:md5,b1518908253a4997fcad98270751112e"
+                        "test_replaced.fasta:md5,b1518908253a4997fcad98270751112e"
                     ]
                 ],
                 "versions_seqkit": [
@@ -45,10 +45,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-12T17:26:01.449665395",
+        "timestamp": "2026-07-01T17:34:12.934060454",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.4"
         }
     },
     "sarscov2 - fasta - uncomp - custom": {
@@ -59,7 +59,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
+                        "test_replaced.fasta:md5,05d3294a62c72f5489f067c1da3c2f6c"
                     ]
                 ],
                 "versions_seqkit": [
@@ -71,10 +71,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-13T12:54:19.323281146",
+        "timestamp": "2026-07-01T17:34:18.009100471",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.4"
         }
     },
     "sarscov2 - fasta - replace": {
@@ -85,7 +85,7 @@
                         {
                             "id": "test"
                         },
-                        "test.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
+                        "test_replaced.fasta.gz:md5,c40eaff961f6f2a48bb7e8fd156ed5d7"
                     ]
                 ],
                 "versions_seqkit": [
@@ -97,10 +97,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-12T17:25:54.471016576",
+        "timestamp": "2026-07-01T17:34:07.395747978",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.3"
+            "nextflow": "26.04.4"
         }
     }
 }
\ No newline at end of file