test.yml

name: test
on:
  push:
    branches: [main]
  pull_request:
    branches: [main]
  merge_group:
    types: [checks_requested]
    branches: [main]
  workflow_dispatch:

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

jobs:
  prettier:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository
        uses: actions/checkout@v3

      - name: Install NodeJS
        uses: actions/setup-node@v3

      - name: Install Prettier
        run: npm install -g prettier

      - name: Run Prettier --check
        run: prettier --check .

  pytest-changes:
    name: pytest-changes
    runs-on: ubuntu-latest
    outputs:
      # Expose matched filters as job 'modules' output variable
      modules: ${{ steps.filter.outputs.changes }}
    steps:
      - uses: actions/checkout@v3

      - uses: dorny/paths-filter@v2
        id: filter
        with:
          filters: "tests/config/pytest_modules.yml"
          token: "${{ secrets.GITHUB_TOKEN }}"

  nf-core-lint:
    runs-on: ubuntu-20.04
    name: nf-core-lint
    needs: [pytest-changes]
    if: needs.pytest-changes.outputs.modules != '[]'
    strategy:
      fail-fast: false
      matrix:
        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
        exclude:
          - tags: "nf-test"
    steps:
      - uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"

      - uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"

      - name: Install pip
        run: python -m pip install --upgrade pip

      - name: Install nf-core tools
        run: python -m pip install nf-core==2.10

      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v1

      - name: Lint module ${{ matrix.tags }}
        run: nf-core modules lint ${{ matrix.tags }}
        if: ${{ !startsWith(matrix.tags, 'subworkflows/') }}

      - name: Remove substring from matrix.tags
        id: remove_substring
        run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT

      - name: Lint subworkflow ${{ matrix.tags }}
        run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}}
        if: ${{ startsWith(matrix.tags, 'subworkflows/') }}

  pytest:
    runs-on: ubuntu-20.04
    name: pytest
    needs: [pytest-changes]
    if: needs.pytest-changes.outputs.modules != '[]'
    strategy:
      fail-fast: false
      matrix:
        tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"]
        profile: ["docker"] #, "singularity", "conda"]
    env:
      NXF_ANSI_LOG: false

    steps:
      - uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"

      - uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install Python dependencies
        run: python -m pip install --upgrade pip -r tests/requirements.txt

      - name: Setup Nextflow ${{ matrix.NXF_VER }}
        uses: nf-core/setup-nextflow@v1
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        uses: eWaterCycle/setup-singularity@v7
        with:
          singularity-version: 3.7.1

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - 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 setup
        if: matrix.profile == 'conda'
        run: |
          conda clean -a
          conda install -n base conda-libmamba-solver
          conda config --set solver libmamba

      # Test the module
      - name: Run pytest-workflow
        # only use one thread for pytest-workflow to avoid race condition on conda cache.
        run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt-get update > /dev/null
          sudo apt-get install bat > /dev/null
          batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}

      - name: Setting global variables
        uses: actions/github-script@v6
        id: parsed
        with:
          script: |
            return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"')
          result-encoding: string

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }}
          path: |
            /home/runner/pytest_workflow_*/*/.nextflow.log
            /home/runner/pytest_workflow_*/*/log.out
            /home/runner/pytest_workflow_*/*/log.err
            /home/runner/pytest_workflow_*/*/work
            !/home/runner/pytest_workflow_*/*/work/conda
            !/home/runner/pytest_workflow_*/*/work/singularity
            !${{ github.workspace }}/.singularity

  nf-test-changes:
    name: nf-test-changes
    runs-on: ubuntu-latest
    outputs:
      # Expose matched filters as job 'modules' output variable
      modules: ${{ steps.filter.outputs.changes }}
    steps:
      - uses: actions/checkout@v3

      - uses: dorny/paths-filter@v2
        id: filter
        with:
          filters: "tests/config/nftest_modules.yml"
          token: "${{ secrets.GITHUB_TOKEN }}"

  nf-test:
    runs-on: ubuntu-20.04
    name: nf-test
    needs: [nf-test-changes]
    if: needs.nf-test-changes.outputs.modules != '[]'
    strategy:
      fail-fast: false
      matrix:
        tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"]
        profile: ["docker"] #, "singularity", "conda"]
    env:
      NXF_ANSI_LOG: false

    steps:
      - uses: actions/checkout@v3

      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v1

      - name: Cache nf-test installation
        id: cache-software
        uses: actions/cache@v3
        with:
          path: |
            /usr/local/bin/nf-test
            /home/runner/.nf-test/nf-test.jar
          key: ${{ runner.os }}-nftest

      - 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@v7
        with:
          singularity-version: 3.7.1

      - name: Set up Singularity
        if: matrix.profile == 'singularity'
        run: |
          mkdir -p $NXF_SINGULARITY_CACHEDIR
          mkdir -p $NXF_SINGULARITY_LIBRARYDIR

      - 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 setup
        if: matrix.profile == 'conda'
        run: |
          conda clean -a
          conda install -n base conda-libmamba-solver
          conda config --set solver libmamba

      # Test the module
      - name: Run nf-test
        run: |
          nf-test test \
            --profile=${{ matrix.profile }} \
            --tag ${{ matrix.tags }} \
            --tap=test.tap

      - uses: pcolby/tap-summary@v1
        with:
          path: >-
            test.tap

  docs-changes:
    runs-on: ubuntu-latest
    outputs:
      docs: ${{ steps.filter.outputs.docs }}
    steps:
      - uses: actions/checkout@v3
      - uses: dorny/paths-filter@v2
        id: filter
        with:
          filters: |
            docs:
              - "docs/**"
              - "**.md"
              - "**.qmd"
              - "**/meta.yml"

  check-docs-render:
    needs: docs-changes
    if: ${{ needs.docs-changes.outputs.docs == 'true' }}
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: quarto-dev/quarto-actions/setup@v2
      - uses: actions/setup-python@v3
      - uses: r-lib/actions/setup-r@v2
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          working-directory: docs/
      - name: Install Python packages
        run: |
          pip install --upgrade pip -r docs/requirements.txt
      - name: prerender
        run: |
          python docs/create-listings.py
      - name: Render without publishing
        uses: quarto-dev/quarto-actions/render@v2

  confirm-pass:
    runs-on: ubuntu-latest
    needs:
      [
        prettier,
        pytest-changes,
        nf-core-lint,
        pytest,
        nf-test-changes,
        nf-test,
        docs-changes,
        check-docs-render,
      ]
    if: always()
    steps:
      - name: All tests ok
        if: ${{ success() || !contains(needs.*.result, 'failure') }}
        run: exit 0
      - name: One or more tests failed
        if: ${{ contains(needs.*.result, 'failure') }}
        run: exit 1

      - name: debug-print
        if: always()
        run: |
          echo "toJSON(needs) = ${{ toJSON(needs) }}"
          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"