CI: add gpu tag test job

.github/workflows/ci.yml

@@ -23,8 +23,101 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
+  nf-test-gpu:
+    name: "Run GPU Tests (${{ matrix.NXF_VER }} | ${{ matrix.profile }})"
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
+    runs-on: "gpu"
+    strategy:
+      fail-fast: false
+      matrix:
+        NXF_VER:
+          - "24.04.2"
+        shard: [1, 2]
+        filter: [pipeline, workflow]
+        profile:
+          - "docker"
+          - "singularity"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "singularity"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: 2
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Python
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        with:
+          python-version: "3.11"
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: "${{ env.NFT_VER }}"
+          install-pdiff: true
+
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
+        shell: bash
+        run: |
+          python -m pip install cryptography
+          nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+
+        # TODO Skip failing conda tests and document their failures
+        # https://github.com/nf-core/modules/issues/7017
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Run GPU Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }})
+        run: |
+          nf-test test \
+              --ci \
+              --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \
+              --changed-since HEAD^ \
+              --profile "+${{ matrix.profile }}" \
+              --filter ${{ matrix.filter }} \
+              --tag "gpu"
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/**/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+
+  nf-test:
+    name: "Run CPU Tests (${{ matrix.NXF_VER }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
     runs-on: ubuntu-latest
@@ -34,13 +127,12 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
-        shard: [1, 2, 3, 4, 5]
+        shard: [1, 2]
         filter: [pipeline, workflow]
         profile:
+          - "conda"
           - "docker"
           - "singularity"
-        test_name:
-          - "test"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -49,6 +141,10 @@ jobs:
             profile: "conda"
           - isMaster: false
             profile: "singularity"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: 2
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -97,14 +193,15 @@ jobs:
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }})
         run: |
           nf-test test \
               --ci \
-              --shard ${{ matrix.shard }}/${{ strategy.job-total }} \
+              --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \
               --changed-since HEAD^ \
               --profile "+${{ matrix.profile }}" \
-              --filter ${{ matrix.filter }}
+              --filter ${{ matrix.filter }} \
+              --tag "cpu"
 
       - name: Output log on failure
         if: failure()

assets/samplesheet_gpu.csv

@@ -0,0 +1,4 @@
+sample,fastq_1,fastq_2,genome
+SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
+SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
+SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,

conf/modules/bwameth_align.config

@@ -1,6 +1,6 @@
 process {
     withName: BWAMETH_ALIGN {
-        cache = 'lenient'
+        cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
         ext.args = ''
         publishDir = [
                 path: { "${params.outdir}/${params.aligner}/alignments" },

conf/modules/parabricks_fq2bammeth.config

@@ -0,0 +1,12 @@
+process {
+    withName: PARABRICKS_FQ2BAMMETH {
+        cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain
+        ext.args = '--low-memory'
+        publishDir = [
+                path: { "${params.outdir}/${params.aligner}/alignments" },
+                pattern: "*.bam",
+                mode: params.publish_dir_mode,
+                enabled: params.save_align_intermeds
+        ]
+    }
+}

conf/subworkflows/fastq_align_dedup_bwameth.config

@@ -1,5 +1,6 @@
 
 includeConfig "../modules/bwameth_align.config"
+includeConfig "../modules/parabricks_fq2bammeth.config"
 includeConfig "../modules/samtools_sort.config"
 includeConfig "../modules/samtools_flagstat.config"
 includeConfig "../modules/samtools_stats.config"

nextflow.config

@@ -221,6 +221,17 @@ profiles {
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
+    docker_self_hosted {
+        docker.enabled      = true
+        docker.fixOwnership = true
+        docker.runOptions   = '--platform=linux/amd64'
+    }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+        use_gpu                 = true
+    }
     test        { includeConfig 'conf/test.config'      }
     test_full   { includeConfig 'conf/test_full.config' }
     test_ci     { params.pipelines_testdata_base_path = './test-datasets/' }

tests/.nftignore

@@ -14,7 +14,7 @@ multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_sources.txt
 multiqc/{bismark,bismark_hisat,bwameth}/multiqc_report.html
 multiqc/{bismark,bismark_hisat,bwameth}/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg}
 pipeline_info/*.{html,json,txt,yml}
-qualimap/**/qualimapReport.html
+{bismark,bismark_hisat,bwameth}/qualimap/bamqc/*/qualimapReport.html
 qualimap/**/css/*
 qualimap/**/images_qualimapReport/*
 qualimap/**/raw_data_qualimapReport/*

tests/bismark_emseq_clip_r1.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | em_seq | clip_r1") {
         when {

tests/bismark_hisat.nf.test

@@ -3,12 +3,13 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark_hisat") {
         when {
             params {
-                aligner        = "bismark_hisat"
-                outdir         = "$outputDir"
+                aligner = "bismark_hisat"
+                outdir  = "$outputDir"
             }
         }
 

tests/bismark_hisat_rrbs.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark_hisat | rrbs") {
         when {

tests/bismark_hisat_save_reference_save_align_intermeds.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark_hisat | save_reference | save_align_intermeds") {
         when {

tests/bismark_nomeseq.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | nomeseq") {
         when {

tests/bismark_rrbs.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | rrbs") {
         when {

tests/bismark_run_preseq.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | run_preseq") {
         when {

tests/bismark_run_qualimap.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | run_qualimap") {
         when {

tests/bismark_run_qualimap.nf.test.snap

@@ -556,7 +556,6 @@
                 "genome_mapping_quality_histogram.png:md5,74776b1e7e8c8876af1cf89d9dbb5f31",
                 "genome_reads_content_per_read_position.png:md5,c6920dc357411880132c207c7d0aa68d",
                 "genome_uniq_read_starts_histogram.png:md5,8f7549a63eee3d3f022699aaa5bb858d",
-                "qualimapReport.html:md5,bbc015c0d1f3c41a08c82fb7a6839039",
                 "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4",
                 "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e",
                 "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25",
@@ -601,7 +600,6 @@
                 "genome_mapping_quality_histogram.png:md5,7ba0db9375d09fd49946b9bca4ba92b4",
                 "genome_reads_content_per_read_position.png:md5,1a6a7717ea948d2518808f72f58ffdef",
                 "genome_uniq_read_starts_histogram.png:md5,395413ab1d0e10af72b116fd8cb12685",
-                "qualimapReport.html:md5,1fe626f663d66a7ce0c6e1e0207d829d",
                 "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803",
                 "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2",
                 "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1",
@@ -643,7 +641,6 @@
                 "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956",
                 "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157",
                 "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19",
-                "qualimapReport.html:md5,af640b29bd28f80bdc0ab6fe7d9c97f4",
                 "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2",
                 "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80",
                 "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8",
@@ -685,7 +682,6 @@
                 "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92",
                 "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de",
                 "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03",
-                "qualimapReport.html:md5,c8114fbb2a63da68111f0d4cbb8a1973",
                 "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce",
                 "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301",
                 "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b",
@@ -752,6 +748,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-28T09:47:26.992492832"
+        "timestamp": "2024-12-02T12:34:53.964190449"
     }
-}
+}

tests/bismark_save_reference_save_align_intermeds.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | save_reference | save_align_intermeds") {
         when {

tests/bismark_skip_deduplication.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | skip_deduplication") {
         when {

tests/bismark_skip_multiqc.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | skip_multiqc") {
         when {

tests/bismark_skip_trimming.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bismark | skip_trimming") {
         when {

tests/bwameth.nf.test

@@ -3,12 +3,13 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bwameth") {
         when {
             params {
-                aligner        = "bwameth"
-                outdir         = "$outputDir"
+                aligner = "bwameth"
+                outdir  = "$outputDir"
             }
         }
 
@@ -18,7 +19,7 @@ nextflow_pipeline {
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
+            def bam_files   = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

tests/bwameth_rrbs.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test Workflow main.nf"
     script "../main.nf"
     config "./nextflow.config"
+    tag "cpu"
 
     test("Params: bwameth | rrbs") {
         when {