diff --git a/modules/nf-core/parabricks/mutectcaller/main.nf b/modules/nf-core/parabricks/mutectcaller/main.nf
index 77552744bb37..7b254940595c 100644
--- a/modules/nf-core/parabricks/mutectcaller/main.nf
+++ b/modules/nf-core/parabricks/mutectcaller/main.nf
@@ -10,6 +10,7 @@ process PARABRICKS_MUTECTCALLER {
     input:
     tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals)
     tuple val(ref_meta), path(fasta)
+    tuple val(fai_meta), path(fasta_fai)
     path panel_of_normals
     path panel_of_normals_index
 
@@ -33,9 +34,13 @@ process PARABRICKS_MUTECTCALLER {
 
     def intervals_command  = intervals     ? (intervals instanceof List ? intervals.collect { interval -> "--interval-file ${interval}" }.join(' ') : "--interval-file ${intervals}") : ""
     def prepon_command = panel_of_normals ? "cp -L ${panel_of_normals_index} `readlink -f ${panel_of_normals}`.tbi && pbrun prepon --in-pon-file ${panel_of_normals}" : ""
-    def postpon_command = panel_of_normals ? "pbrun postpon --in-vcf ${prefix}.vcf.gz --in-pon-file ${panel_of_normals} --out-vcf ${prefix}_annotated.vcf.gz" : ""
+    // pbrun postpon requires uncompressed .vcf input; output uncompressed when PON is provided
+    def mutect_out     = panel_of_normals ? "${prefix}.vcf"    : "${prefix}.vcf.gz"
+    def stats_rename   = panel_of_normals ? "mv ${prefix}.vcf.stats ${prefix}.vcf.gz.stats" : ""
+    def postpon_command = panel_of_normals ? "pbrun postpon --in-vcf ${prefix}.vcf --in-pon-file ${panel_of_normals} --out-vcf ${prefix}.vcf.gz" : ""
 
     def num_gpus = task.accelerator ? "--num-gpus ${task.accelerator.request}" : ""
+    def normal_bam_flag = normal_bam ? "--in-normal-bam ${normal_bam}" : ""
     """
     # if panel of normals specified, run prepon
     ${prepon_command}
@@ -44,23 +49,22 @@ process PARABRICKS_MUTECTCALLER {
         mutectcaller \\
         --ref ${fasta} \\
         --in-tumor-bam ${tumor_bam} \\
-        --tumor-name ${meta.tumor_id} \\
-        --out-vcf ${prefix}.vcf.gz \\
+        ${normal_bam_flag} \\
+        --out-vcf ${mutect_out} \\
         ${intervals_command} \\
         ${num_gpus} \\
         ${args}
 
-    # if panel of normals specified, run postpon
+    # if panel of normals specified, rename stats and run postpon
+    ${stats_rename}
     ${postpon_command}
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def postpon_command = panel_of_normals ? "echo '' | gzip > ${prefix}_annotated.vcf.gz" : ""
     """
     echo "" | gzip > ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.stats
-    ${postpon_command}
 
     # Capture the full version output once and store it in a variable
     pbrun_version_output=\$(pbrun mutectcaller --version 2>&1)
diff --git a/modules/nf-core/parabricks/mutectcaller/meta.yml b/modules/nf-core/parabricks/mutectcaller/meta.yml
index 7e0972221070..6360c346b240 100644
--- a/modules/nf-core/parabricks/mutectcaller/meta.yml
+++ b/modules/nf-core/parabricks/mutectcaller/meta.yml
@@ -61,6 +61,16 @@ input:
         description: reference fasta - must be unzipped.
         pattern: "*.fasta"
         ontologies: []
+  - - fai_meta:
+        type: map
+        description: |
+          Groovy Map containing reference index information
+          [ id:'homo_sapiens' ]
+    - fasta_fai:
+        type: file
+        description: reference fasta index - required when input is in CRAM format.
+        pattern: "*.fai"
+        ontologies: []
   - panel_of_normals:
       type: file
       description: (Optional) panel of normals file.
diff --git a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
index d75b2763ce9c..5a2c2a50555e 100644
--- a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
+++ b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = "--mutect-low-memory"
+                module_args = "--tumor-name tumour --mutect-low-memory"
             }
             process {
                 """
@@ -32,8 +32,12 @@ nextflow_process {
                     [ id: 'reference' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                     ]
-                input[2] = [] // pon
-                input[3] = [] // pon index
+                input[2] = [ // fasta_fai
+                    [ id: 'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                    ]
+                input[3] = [] // pon
+                input[4] = [] // pon index
                 """
             }
         }
@@ -100,7 +104,7 @@ nextflow_process {
 
     //     when {
     //         params {
-    //             module_args = "--mutect-low-memory"
+    //             module_args = "--tumor-name tumour --mutect-low-memory"
     //         }
     //         process {
     //             """
@@ -227,7 +231,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = "--mutect-low-memory"
+                module_args = "--tumor-name tumour --mutect-low-memory"
             }
             process {
                 """
@@ -243,8 +247,12 @@ nextflow_process {
                     [ id: 'reference' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                     ]
-                input[2] = [] // pon
-                input[3] = [] // pon index
+                input[2] = [ // fasta_fai
+                    [ id: 'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                    ]
+                input[3] = [] // pon
+                input[4] = [] // pon index
                 """
             }
         }
@@ -283,8 +291,12 @@ nextflow_process {
                     [ id: 'reference' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
                     ]
-                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
-                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
+                input[2] = [ // fasta_fai
+                    [ id: 'reference' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                    ]
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi', checkIfExists: true)
                 """
             }
         }
diff --git a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap
index f4bc60a6fd26..8a90bb4ac47e 100644
--- a/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap
+++ b/modules/nf-core/parabricks/mutectcaller/tests/main.nf.test.snap
@@ -8,10 +8,7 @@
                             "id": "test",
                             "tumor_id": "tumour"
                         },
-                        [
-                            "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -51,10 +48,7 @@
                             "id": "test",
                             "tumor_id": "tumour"
                         },
-                        [
-                            "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_annotated.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions_parabricks": [
@@ -70,7 +64,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-21T13:36:25.252321993"
+        "timestamp": "2026-05-14T09:11:19.859893899"
     },
     "human - bam - stub": {
         "content": [