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: "0.7.3"

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

jobs:
  changes:
    name: Check for changes
    runs-on: ubuntu-latest
    outputs:
      # Expose matched filters as job 'tags' output variable
      tags: ${{ steps.filter.outputs.changes }}
    steps:
      - uses: actions/checkout@v3
      - uses: dorny/paths-filter@v2
        id: filter
        with:
          filters: "tests/config/tags.yml"

  define_nxf_versions:
    name: Choose nextflow versions to test against depending on target branch
    runs-on: ubuntu-latest
    outputs:
      matrix: ${{ steps.nxf_versions.outputs.matrix }}
    steps:
      - id: nxf_versions
        run: |
          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
          else
            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
          fi

  test-dev:
    if: (github.base_ref == 'dev' || (github.event_name == 'push'))
    name: ${{ matrix.tags }} ${{ matrix.profile }} NXF ${{ matrix.NXF_VER }}
    runs-on: ubuntu-latest
    needs: changes
    strategy:
      fail-fast: false
      matrix:
        # Run tests based on changes in code
        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
        # Only run docker tests on dev branch
        profile: ["docker"]
        # Only test minimal version
        NXF_VER: ["23.04.0"]
        # Always run default test
        include:
          - tags: default

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

      - uses: actions/cache@v3
        with:
          path: /usr/local/bin/nextflow
          key: ${{ runner.os }}
          restore-keys: |
            ${{ runner.os }}-nextflow-

      - name: Install nf-test
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
          sudo mv nf-test /usr/local/bin/

      - name: Install Nextflow ${{ matrix.NXF_VER }}
        uses: nf-core/setup-nextflow@v1.2.0
        with:
          version: "${{ matrix.NXF_VER }}"

      - name: Run nf-test
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: nf-test test tests/pipeline/${{ matrix.tags }}.nf.test --profile "test,${{ matrix.profile }}" --tap=test.tap
          attempt_limit: 3

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

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-${{ matrix.profile }}
          path: |
            /home/runner/pytest_workflow_*/*/.nextflow.log
            /home/runner/pytest_workflow_*/*/log.out
            /home/runner/pytest_workflow_*/*/log.err
            /home/runner/pytest_workflow_*/*/work

  test-master:
    # Only run on master branch or when a PR is opened against master
    if: github.base_ref == 'master'
    name: ${{ matrix.tags }} ${{ matrix.profile }} NXF ${{ matrix.NXF_VER }}
    runs-on: ubuntu-latest
    needs: [changes, define_nxf_versions]
    strategy:
      fail-fast: false
      matrix:
        # Run tests based on changes in code
        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
        # Only run docker tests on dev branch
        profile: ["docker", "singularity", "conda"]
        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
        # Always run default test
        include:
          - tags: default

    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - uses: actions/cache@v3
        with:
          path: /usr/local/bin/nextflow
          key: ${{ runner.os }}
          restore-keys: |
            ${{ runner.os }}-nextflow-

      - name: Install nf-test
        run: |
          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
          sudo mv nf-test /usr/local/bin/

      - name: Install Nextflow ${{ matrix.NXF_VER }}
        uses: nf-core/setup-nextflow@v1.2.0
        with:
          version: "${{ matrix.NXF_VER }}"

      - 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
        uses: Wandalen/wretry.action@v1.0.11
        with:
          command: nf-test test tests/pipeline/${{ matrix.tag }}.nf.test --profile "test,${{ matrix.profile }}" --tap=test.tap
          attempt_limit: 3

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

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-${{ matrix.profile }}
          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