diff --git a/modules/nf-core/pbmm2/align/main.nf b/modules/nf-core/pbmm2/align/main.nf
index e993f7760610..5a545a6ff9b9 100644
--- a/modules/nf-core/pbmm2/align/main.nf
+++ b/modules/nf-core/pbmm2/align/main.nf
@@ -24,10 +24,21 @@ process PBMM2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    fasta="${fasta}"
+    if [[ \${fasta} == *.fna ]]; then
+        new_name=\${fasta%.fna}.fa
+        mv \${fasta} \${new_name}
+        fasta=\${new_name}
+    elif [[ \${fasta} == *.fna.gz ]]; then
+        new_name=\${fasta%.fna.gz}.fa.gz
+        mv \${fasta} \${new_name}
+        fasta=\${new_name}
+    fi
+
     pbmm2 \\
         align \\
         $args \\
-        $fasta \\
+        \${fasta} \\
         $bam \\
         ${prefix}.bam \\
         --num-threads ${task.cpus}
diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test b/modules/nf-core/pbmm2/align/tests/main.nf.test
index a753ddb6a9ba..5fac28d120dc 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test
@@ -37,7 +37,33 @@ nextflow_process {
 
     }
 
-    test("pbmm2  - bam - stub") {
+    test("pbmm2 - bam - fna") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("pbmm2 - bam - stub") {
 
         options "-stub"
 
diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
index 5fd660139695..4b465725fe36 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
@@ -27,13 +27,47 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-31T09:41:49.070164992",
+        "timestamp": "2026-08-26T11:17:08.217985366",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.07.0"
+            "nextflow": "26.04.6"
         }
     },
-    "pbmm2  - bam - stub": {
+    "pbmm2 - bam - fna": {
+        "content": [
+            {
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,85fc597755dd2aca64e9141248fac2e0"
+                    ]
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d19601b196d069d281c0280bbb6dda6f"
+                    ]
+                ],
+                "versions_pbmm2": [
+                    [
+                        "PBMM2_ALIGN",
+                        "pbmm2",
+                        "26.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-26T11:17:26.093538311",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "pbmm2 - bam - stub": {
         "content": [
             {
                 "bam": [
@@ -61,10 +95,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-31T09:24:42.692283981",
+        "timestamp": "2026-08-26T09:49:08.199180076",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.07.0"
+            "nextflow": "26.04.6"
         }
     }
 }
\ No newline at end of file