ci.yml

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
  pull_request:
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false
  NFT_VER: "0.8.4"
  NFT_WORKDIR: "~"
  NFT_DIFF: "pdiff"
  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"

concurrency:
  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
  cancel-in-progress: true
jobs:
  nf-test-changes:
    name: Check for changes
    runs-on: ubuntu-latest
    outputs:
      nf_test_files: ${{ steps.list.outputs.nf_test_files }}
    steps:
      - uses: actions/setup-python@v4
        with:
          python-version: "3.11"
          architecture: "x64"
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install gitpython pyyaml

      - name: list nf_test_files
        id: list
        run: |
          echo nf_test_files=$(python \
            .github/python/find_changed_files.py \
            -t pipeline workflow process \
            --head_ref ${{ github.sha }} \
            --base_ref origin/${{ github.base_ref }} \
          ) >> $GITHUB_OUTPUT

      - name: debug
        run: |
          echo ${{ steps.list.outputs.nf_test_files }}

  test:
    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
    needs: [nf-test-changes]
    if: needs.nf-test-changes.outputs.nf_test_files != '[]'
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER:
          - "latest-everything"
          - "23.04"
        nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
        profile:
          - "docker"

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v4

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ matrix.NXF_VER }}"

      - uses: actions/setup-python@v4
        with:
          python-version: "3.11"
          architecture: "x64"

      - name: Install pdiff to see diff between nf-test snapshots
        run: |
          python -m pip install --upgrade pip
          pip install pdiff

      - 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: ${{ runner.os }}-${{ env.NFT_VER }}-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: Run nf-test
        run: |
          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap

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

      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/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

  confirm-pass:
    runs-on: ubuntu-latest
    needs: [test]
    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) }}"