nf-test.yml

name: Run nf-test
on:
  pull_request:
    branches: [master]
  merge_group:
    types: [checks_requested]
    branches: [master]
  workflow_dispatch:
    inputs:
      runners:
        description: "Runners to test on"
        type: choice
        options:
          - "ubuntu-latest"
          - "self-hosted"
        default: "self-hosted"

# 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:
  nf-test:
    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
    # NOTE I think this is the cleanest way to get them organized
    # process | conda | 1
    # process | conda | 2
    # process | conda | 3
    # process | docker_self_hosted | 1
    # ...
    # workflow | singularity | 3
    name: ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }}
    strategy:
      fail-fast: false
      matrix:
        filter: [process, workflow]
        profile: [conda, docker_self_hosted, singularity]
        shard: [1, 2, 3]
    env:
      NXF_ANSI_LOG: false
      NXF_VER: "24.04.4"
      NFTEST_VER: "0.9.0"
      TOTAL_SHARDS: 3
      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}

    steps:
      # TODO If conda-fail.yml exists and matrix = conda skip
      # https://github.com/askimed/nf-test/issues/260

      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
        with:
          fetch-depth: 0

      - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4
        with:
          distribution: "temurin"
          java-version: "17"
      - name: Setup Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: ${{ env.NXF_VER }}

      - name: Install nf-test
        uses: nf-core/setup-nf-test@v1
        with:
          version: ${{ env.NFTEST_VER }}

      - name: Setup 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

      - name: Set up Python
        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
        with:
          python-version: "3.11"

      - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
        id: cache-pip-pdiff
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-pdiff
          restore-keys: |
            ${{ runner.os }}-pip-pdiff

      - name: Install Python dependencies
        run: python -m pip install --upgrade pip pdiff cryptography

      - name: Set up miniconda
        if: matrix.profile == 'conda'
        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
        with:
          miniconda-version: "latest"
          auto-update-conda: true
          channels: conda-forge,bioconda,defaults

      - name: Conda setup
        if: matrix.profile == 'conda'
        run: |
          conda clean -a
          conda install -n base conda-libmamba-solver
          conda config --set solver libmamba
          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
          echo $(realpath python) >> $GITHUB_PATH

      # Set up secrets
      - name: Set up nextflow secrets
        # TODO Only run if the tag includes `sentieon`
        if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null
        run: |
          nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")

      # Test the module
      - name: Run Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }})
        env:
          NFT_DIFF: "pdiff"
          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
          SENTIEON_AUTH_MECH: "GitHub Actions - token"
        run: |
          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
          if [ "${{ matrix.profile }}" == "docker" ]; then
            PROFILE="docker_self_hosted"
          else
            PROFILE=${{ matrix.profile }}
          fi

          NFT_WORKDIR=~ \
          nf-test test \
            --profile=${{ matrix.profile }} \
            --tap=test.tap \
            --ci \
            --verbose \
            --only-changed \
            --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \
            --filter ${{ matrix.filter }} \
            --follow-dependencies

      # TODO If matrix == conda create a conda-fail.yml and commit it

      # TODO If no test.tap, then make one to spoof?
      # - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
      #   with:
      #     path: >-
      #       test.tap

      - name: Clean up
        if: always()
        run: |
          sudo rm -rf /home/ubuntu/tests/