diff --git a/CHANGELOG.md b/CHANGELOG.md
index 904e348f..fef97e7d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Pipeline Updates
 
--
+- 🔧 Removed parameter `use_gpu`. Adding the `gpu` profile with `--profile gpu` is adequate to activate the GPU-based pathways [#520](https://github.com/nf-core/methylseq/pull/520)
 
 ## [v3.0.0](https://github.com/nf-core/methylseq/releases/tag/3.0.0) - [2024-12-16]
 
diff --git a/README.md b/README.md
index cf30cb9a..e3725502 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).
 
-Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `--use_gpu` flag along with `--aligner bwameth`.
+Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `gpu` profile along with `--aligner bwameth`.
 
 | Step                                         | Bismark workflow         | bwa-meth workflow     |
 | -------------------------------------------- | ------------------------ | --------------------- |
diff --git a/docs/usage.md b/docs/usage.md
index c750a6b3..08acbd77 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -34,7 +34,7 @@ bwa-meth aligner options:
 
 - Standard `bwa-meth` (CPU-based): This option can be invoked via `--aligner bwameth` and uses the traditional BWA-Meth aligner and runs on CPU processors.
 
-- `Parabricks/FQ2BAMMETH` (GPU-based): For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `--use_gpu` flag along with `--aligner bwameth`.
+- `Parabricks/FQ2BAMMETH` (GPU-based): For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `gpu` profile (as in `--profile gpu`) along with `--aligner bwameth`.
 
 ## Samplesheet input
 
diff --git a/modules.json b/modules.json
index af2a9655..dad1add5 100644
--- a/modules.json
+++ b/modules.json
@@ -156,7 +156,7 @@
                     },
                     "fastq_align_dedup_bwameth": {
                         "branch": "master",
-                        "git_sha": "bd5f75ccaf2345269810e66e85de8a70e4de8764",
+                        "git_sha": "e55eae4a09b659522cf1b7898b5644fe06f66198",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
diff --git a/nextflow.config b/nextflow.config
index de859e8e..55127408 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -75,7 +75,6 @@ params {
     nomeseq                      = false
 
     // bwa-meth options
-    use_gpu                      = false
     min_depth                    = 0
     ignore_flags                 = false
     methyl_kit                   = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 57849217..581043a4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -380,12 +380,6 @@
             "description": "",
             "default": "",
             "properties": {
-                "use_gpu": {
-                    "type": "boolean",
-                    "description": "Run Parabricks GPU-accelerated fq2bammeth module for alignment",
-                    "default": false,
-                    "fa_icon": "fas fa-dot-circle"
-                },
                 "min_depth": {
                     "type": "integer",
                     "description": "Specify a minimum read coverage for MethylDackel to report a methylation call.",
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf
index c0cc67b8..90488250 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf
@@ -17,6 +17,7 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH {
     ch_fasta_index       // channel: [ val(meta), [ fasta index ] ]
     ch_bwameth_index     // channel: [ val(meta), [ bwameth index ] ]
     skip_deduplication   // boolean: whether to deduplicate alignments
+    use_gpu              // boolean: whether to use GPU or CPU for bwameth alignment
 
     main:
 
@@ -34,7 +35,7 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH {
     /*
      * Align with bwameth
      */
-    if (params.use_gpu) {
+    if (use_gpu) {
         /*
         * Align with parabricks GPU enabled fq2bammeth implementation of bwameth
         */
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml
index a66ea024..353d9322 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml
@@ -49,6 +49,10 @@ input:
       type: boolean
       description: |
         Skip deduplication of aligned reads
+  - use_gpu:
+      type: boolean
+      description: |
+        Use GPU for alignment
 output:
   - bam:
       type: file
@@ -114,3 +118,4 @@ authors:
   - "@sateeshperi"
 maintainers:
   - "@sateeshperi"
+  - "@gallvp"
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test
index b156de6b..039bc4f0 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test
@@ -38,10 +38,6 @@ nextflow_workflow {
     test("Params: parabricks/fq2bammeth single-end | use_gpu") {
 
         when {
-            params {
-                skip_deduplication = false
-                use_gpu            = true
-            }
 
             workflow {
                 """
@@ -58,7 +54,8 @@ nextflow_workflow {
                             file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
                 ])
                 input[3] = UNTAR.out.untar
-                input[4] = params.skip_deduplication
+                input[4] = false // skip_deduplication
+                input[5] = true // use_gpu
                 """
             }
         }
@@ -105,7 +102,8 @@ nextflow_workflow {
                             file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
                 ])
                 input[3] = UNTAR.out.untar
-                input[4] = params.skip_deduplication
+                input[4] = true // skip_deduplication
+                input[5] = true // use_gpu
                 """
             }
         }
@@ -129,4 +127,4 @@ nextflow_workflow {
         }
     }
 
-}
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test
index 6b20d545..e644892d 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test
@@ -37,10 +37,6 @@ nextflow_workflow {
     test("Params: bwameth single-end | default") {
 
         when {
-            params {
-                skip_deduplication = false
-                use_gpu            = false
-            }
 
             workflow {
                 """
@@ -57,7 +53,8 @@ nextflow_workflow {
                             file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
                 ])
                 input[3] = UNTAR.out.untar
-                input[4] = params.skip_deduplication
+                input[4] = false // skip_deduplication
+                input[5] = false // use_gpu
                 """
             }
         }
@@ -84,10 +81,6 @@ nextflow_workflow {
     test("Params: bwameth paired-end | default") {
 
         when {
-            params {
-                skip_deduplication = false
-                use_gpu            = false
-            }
 
             workflow {
                 """
@@ -105,7 +98,8 @@ nextflow_workflow {
                             file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
                 ])
                 input[3] = UNTAR.out.untar
-                input[4] = params.skip_deduplication
+                input[4] = false // skip_deduplication
+                input[5] = false // use_gpu
                 """
             }
         }
@@ -132,10 +126,6 @@ nextflow_workflow {
     test("Params: bwameth paired-end | skip_deduplication") {
 
         when {
-            params {
-                skip_deduplication = true
-                use_gpu            = false
-            }
 
             workflow {
                 """
@@ -153,7 +143,8 @@ nextflow_workflow {
                             file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
                 ])
                 input[3] = UNTAR.out.untar
-                input[4] = params.skip_deduplication
+                input[4] = true // skip_deduplication
+                input[5] = false // use_gpu
                 """
             }
         }
@@ -176,4 +167,4 @@ nextflow_workflow {
             )
         }
     }
-}
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap
index 90c96015..3a35462e 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                 ]
             ],
             [
-
+                
             ],
             [
                 [
@@ -110,7 +110,7 @@
                 ]
             ],
             [
-
+                
             ],
             [
                 [
@@ -122,7 +122,7 @@
                 ]
             ],
             [
-
+                
             ],
             [
                 "test.flagstat",
@@ -182,7 +182,7 @@
                 ]
             ],
             [
-
+                
             ],
             [
                 [
@@ -221,4 +221,4 @@
         },
         "timestamp": "2024-11-17T05:42:39.183331191"
     }
-}
+}
\ No newline at end of file
diff --git a/tests/bwameth_use_gpu.nf.test b/tests/bwameth_use_gpu.nf.test
index 9da5074b..61d30da8 100644
--- a/tests/bwameth_use_gpu.nf.test
+++ b/tests/bwameth_use_gpu.nf.test
@@ -11,7 +11,6 @@ nextflow_pipeline {
             params {
                 input   = "${projectDir}/assets/samplesheet_gpu.csv"
                 aligner = "bwameth" // uses parabricks/fq2bammeth
-                use_gpu = true
                 outdir  = "$outputDir"
             }
         }
diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf
index e4d2edf7..371903c5 100644
--- a/workflows/methylseq/main.nf
+++ b/workflows/methylseq/main.nf
@@ -120,6 +120,7 @@ workflow METHYLSEQ {
             ch_fasta_index,
             ch_bwameth_index,
             params.skip_deduplication || params.rrbs,
+            workflow.profile.tokenize(',').intersect(['gpu']).size() >= 1
         )
         ch_bam         = FASTQ_ALIGN_DEDUP_BWAMETH.out.bam
         ch_bai         = FASTQ_ALIGN_DEDUP_BWAMETH.out.bai