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:
    branches:
      - dev
      - master
  release:
    types: [published]

env:
  NXF_ANSI_LOG: false
  CAPSULE_LOG: none
  NFTEST_VER: "0.8.2"

concurrency:
  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
  cancel-in-progress: true

jobs:
  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:
    name: Run pipeline with test data
    needs: define_nxf_versions
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
        profile:
          - docker
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

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

      # Install nf-test
      - 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/

      # Run nf-test
      - name: Run nf-test
        run: nf-test test tests/pipeline/ --profile=test,${{ matrix.profile }} --junitxml=test.xml

      # If the test fails, output the software_versions.yml using the 'batcat' utility
      - name: Output log on failure
        if: failure()
        run: |
          sudo apt install bat > /dev/null
          batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml

      - 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
