TCRtoolkit/.github/workflows/nextflow-test.yaml at main · KarchinLab/TCRtoolkit · GitHub

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#inspired by https://docs.cirro.bio/pipelines/development/#automated-testing
name: Nextflow Tests

on:
  pull_request:
      branches:
      - 'main'
  workflow_dispatch:

jobs:
  unit-tests:
    name: Unit Tests
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        with:
          submodules: recursive

      - name: Setup Java
        uses: actions/setup-java@v2
        with:
          distribution: 'temurin'
          java-version: '17'

      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      - name: Install nf-test
        run: |
          wget -qO- https://get.nf-test.com | bash
          sudo mv nf-test /usr/local/bin

      - name: Run unit tests
        run: nf-test test tests/modules/ --verbose --junitxml=unit-test-results.xml

      - name: Publish unit test results
        if: always()
        uses: EnricoMi/publish-unit-test-result-action@v2
        with:
          files: unit-test-results.xml
          check_name: Unit Test Results

      - name: Upload unit test results
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: unit-test-results
          path: |
            .nf-test/tests/
            unit-test-results.xml

  pipeline-test:
    name: Pipeline Integration Test
    runs-on: ubuntu-latest
    needs: unit-tests
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
        with:
          submodules: recursive

      - name: Setup Java
        uses: actions/setup-java@v2
        with:
          distribution: 'temurin'
          java-version: '17'

      - name: Install Nextflow
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      - name: Install nf-test
        run: |
          wget -qO- https://get.nf-test.com | bash
          sudo mv nf-test /usr/local/bin

      - name: Run pipeline test
        run: nf-test test tests/main.nf.test --verbose --junitxml=pipeline-test-results.xml