diff --git a/.github/conda_skip.yml b/.github/conda_skip.yml
index 14da877f04d..5e6c646e1e6 100644
--- a/.github/conda_skip.yml
+++ b/.github/conda_skip.yml
@@ -184,3 +184,5 @@ exclude:
     path: modules/nf-core/xeniumranger/import-segmentation
   - profile: conda
     path: modules/nf-core/parabricks/genotypegvcf
+  - profile: conda
+    path: modules/nf-core/parabricks/applybqsr
diff --git a/modules/nf-core/parabricks/applybqsr/main.nf b/modules/nf-core/parabricks/applybqsr/main.nf
index 38b2af002b8..c4900b3f14f 100644
--- a/modules/nf-core/parabricks/applybqsr/main.nf
+++ b/modules/nf-core/parabricks/applybqsr/main.nf
@@ -2,8 +2,9 @@ process PARABRICKS_APPLYBQSR {
     tag "$meta.id"
     label 'process_high'
     label 'process_gpu'
+    stageInMode 'copy'
 
-    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1"
+    container "nvcr.io/nvidia/clara/clara-parabricks:4.4.0-1"
 
     input:
     tuple val(meta), path(bam)
@@ -28,13 +29,8 @@ process PARABRICKS_APPLYBQSR {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
-    def copy_index_command = bam_index ? "cp -L $bam_index `readlink -f $bam`.bai" : ""
     def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
-    # parabricks complains when index is not a regular file in the same directory as the bam
-    # copy the index to this path.
-    $copy_index_command
-
     pbrun \\
         applybqsr \\
         --ref $fasta \\
@@ -53,9 +49,7 @@ process PARABRICKS_APPLYBQSR {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
     """
     touch ${prefix}.bam
     touch ${prefix}.bam.bai
diff --git a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
index c7a55002ac5..e90a1d51324 100644
--- a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
+++ b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
@@ -4,42 +4,42 @@
             "2f11e4fe3390b8ad0a1852616fd1da04",
             "test.bam.bai",
             [
-                "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                "versions.yml:md5,f396830824c06b6dc30056e423a91634"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-31T08:40:58.540517299"
+        "timestamp": "2024-12-10T08:44:34.058228768"
     },
     "sarscov2 - bam - pe": {
         "content": [
             "894549ee3ced6b5ca2eed2563a985217",
             "test.bam.bai",
             [
-                "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                "versions.yml:md5,f396830824c06b6dc30056e423a91634"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-30T10:55:02.759938278"
+        "timestamp": "2024-12-10T08:44:17.204736211"
     },
     "sarscov2 - bam - pe - intervals": {
         "content": [
             "b194021b699cc5cf4b2b1f715e0b7b4c",
             "test.bam.bai",
             [
-                "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                "versions.yml:md5,f396830824c06b6dc30056e423a91634"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-30T11:20:43.476752722"
+        "timestamp": "2024-12-10T08:44:25.661590103"
     },
     "sarscov2 - bam - pe - intervals - stub": {
         "content": [
@@ -61,7 +61,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                    "versions.yml:md5,f396830824c06b6dc30056e423a91634"
                 ],
                 "bai": [
                     [
@@ -80,15 +80,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                    "versions.yml:md5,f396830824c06b6dc30056e423a91634"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-30T11:21:02.658767469"
+        "timestamp": "2024-12-10T08:44:47.700907318"
     },
     "human - cram - pe - intervals - stub": {
         "content": [
@@ -110,7 +110,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                    "versions.yml:md5,f396830824c06b6dc30056e423a91634"
                 ],
                 "bai": [
                     [
@@ -129,14 +129,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                    "versions.yml:md5,f396830824c06b6dc30056e423a91634"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-30T11:20:56.908929981"
+        "timestamp": "2024-12-10T08:44:41.08456539"
     }
 }
\ No newline at end of file