Count NTC reads in sequencing QC check (#531)(patch) #174
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| name: 'Merge-master-CI' | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| - 'main' | |
| jobs: | |
| bump-version: | |
| runs-on: ubuntu-latest | |
| name: Bump version and push tags to master | |
| steps: | |
| - name: Bump version | |
| uses: Clinical-Genomics/bump2version-ci@master | |
| env: | |
| BUMPVERSION_TOKEN: ${{ secrets.BUMPVERSION_TOKEN }} | |
| BUMPVERSION_AUTHOR: ${{ secrets.BUMPVERSION_AUTHOR }} | |
| BUMPVERSION_EMAIL: ${{ secrets.BUMPVERSION_EMAIL }} | |
| GITHUB_REPOSITORY: ${{ github.repository }} | |
| docker-image-push: | |
| runs-on: ubuntu-latest | |
| name: Push staging docker image to dockerhub | |
| steps: | |
| - name: Check out git repository | |
| uses: actions/checkout@v2 | |
| - name: Extract branch name and remove illegal chars | |
| id: get_branch_name | |
| shell: bash | |
| run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Set up Docker Buildx | |
| id: buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build and push | |
| id: docker_build | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: ./ | |
| file: ./Dockerfile | |
| push: true | |
| tags: "clinicalgenomics/cg_lims-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/cg_lims-stage:latest" | |
| tests-coverage: | |
| runs-on: ubuntu-latest | |
| name: Test and coveralls | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Check out limsmock | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: "Clinical-Genomics/limsmock" | |
| - name: Install limsmock dependencies | |
| run: | | |
| python -m pip install --upgrade pip==21.1.2 | |
| pip install -r requirements.txt -r requirements-dev.txt . | |
| - name: Check out cg_lims | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: "Clinical-Genomics/cg_lims" | |
| - name: Install cg_lims dependencies | |
| run: | | |
| pip install -r requirements.txt -r requirements-dev.txt . | |
| - name: Install coveralls dependencies | |
| run: | | |
| pip install pytest-cov coveralls | |
| - name: Test with pytest & Coveralls | |
| run: | | |
| pytest --cov=cg_lims/ | |
| coveralls | |
| env: | |
| GITHUB: 1 | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} |