ci.yml

# 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"
  pull_request:
    branches:
      - "dev"
      - "master"
  release:
    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
        with:
          token: "${{ secrets.GITHUB_TOKEN }}"

      - 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: ${{ matrix.tags }} (${{ matrix.profile }}-${{ matrix.NXF_VER }})
    # Only run on push if this is the nf-core dev branch (merged PRs)
    if: needs.list.outputs.tests != '[]'
    needs: [list]
    runs-on: ubuntu-latest
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
        profile: ["docker"] # TODO , "singularity", "conda"]
        test: ["${{ 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: "${{ matrix.NXF_VER }}"
          token: "${{ secrets.GITHUB_TOKEN }}"

      - 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: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml