Merge branch 'dev' into bump/parabricks_mem

sateeshperi · web-flow · commit 90e3ba5fd4b1 · 2025-05-24T18:00:00.000-07:00
diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml
@@ -30,7 +30,9 @@ env:
 
 jobs:
   get-shards:
-    runs-on: "runs-on=${{ github.run_id }}/family=g4dn.xlarge/image=ubuntu24-gpu-x64"
+    runs-on:
+      - runs-on=${{ github.run_id }}-nf-test-get-shards-gpu
+      - runner=2cpu-linux-x64
     name: "Get Shards"
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -86,6 +88,10 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Test CUDA
+        run: |
+          nvidia-smi -L
+
       - name: Run nf-test Action
         uses: ./.github/actions/nf-test
         with:
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -35,7 +35,7 @@ jobs:
   get-shards:
     runs-on:
       - runs-on=${{ github.run_id }}-nf-test-get-shards
-      - runner=4cpu-linux-x64
+      - runner=2cpu-linux-x64
     name: "Get Shards"
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,7 +13,7 @@ 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml
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
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
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
diff --git a/tests/bwameth_use_gpu.nf.test b/tests/bwameth_use_gpu.nf.test
@@ -6,11 +6,11 @@ nextflow_pipeline {
     tag "gpu"
 
     test("Params: bwameth | use_gpu") {
+
         when {
             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
@@ -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
