Merge branch 'dev' into nf-core-template-merge-2.11

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @nf-core/methylseq

.github/workflows/awsfulltest.yml

@@ -12,12 +12,12 @@ jobs:
     name: Run AWS full tests
     if: github.repository == 'nf-core/methylseq'
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["bismark", "bismark_hisat", "bwameth"]
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -27,7 +27,8 @@ jobs:
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}/${{matrix.aligner}}"
+              "aligner": "${{ matrix.aligner }}",
             }
           profiles: test_full
 

.github/workflows/awstest.yml

@@ -9,6 +9,9 @@ jobs:
     name: Run AWS tests
     if: github.repository == 'nf-core/methylseq'
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["bismark", "bismark_hisat", "bwameth"]
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
@@ -21,7 +24,8 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-test-${{ github.sha }}"
+              "aligner": "${{ matrix.aligner }}",
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-test-${{ github.sha }}/${{matrix.aligner}}"
             }
           profiles: test
 

.github/workflows/ci.yml

@@ -1,43 +1,124 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
   push:
     branches:
-      - dev
+      - "dev"
   pull_request:
+    branches:
+      - "dev"
+      - "master"
   release:
-    types: [published]
+    types:
+      - "published"
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
+  list:
+    name: List Tests
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      tests: ${{ steps.list.outputs.tests }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: List nf-test
+        id: list
+        run: |
+          echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT"
+
   test:
-    name: Run pipeline with test data
+    name: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }})
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}"
+    if: needs.list.outputs.tests != '[]'
+    needs: [list]
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        profile: ["docker"] # TODO , "singularity", "conda"]
+        test: ["${{ fromJson(needs.list.outputs.tests) }}"]
+        exclude:
+          - test: "tests/subworkflows/local/grohmm/main.nf.test@3508b8c9"
+          - test: "tests/subworkflows/local/grohmm/main.nf.test@716555be"
+          - test: "tests/subworkflows/local/grohmm/main.nf.test@306b4b15"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
 
+      - name: Cache Nextflow installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }}
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
+
+      - name: Run nf-test
+        run: |
+          nf-test test \
+            --profile="test,${{ matrix.profile }}" \
+            ${{ matrix.test }} \
+            --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: success() || failure() # run this step even if previous step failed
+        with:
+          path: ${{ matrix.test }}-${{ matrix.profile }}.xml
+
+      - name: Output log on failure
+        if: failure()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml

.gitignore

@@ -6,3 +6,7 @@ results/
 testing/
 testing*
 *.pyc
+.vscode
+.nf-test
+.nf-test.log
+test-datasets/

.nf-core.yml

@@ -1 +1,8 @@
 repository_type: pipeline
+lint:
+  files_unchanged:
+    - .gitattributes
+  files_exist:
+    - bin/markdown_to_html.py
+  actions_ci: False
+  multiqc_config: False

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+*.nf.test.snap