loooooong nose #5577
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| # Continuous integration test of any branch. | |
| name: CI | |
| on: | |
| push: | |
| branches-ignore: | |
| - main | |
| jobs: | |
| # Run Python tests on Github runner | |
| tox_test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7] | |
| steps: | |
| - name: Checkout github repo (+ download lfs dependencies) | |
| uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Checkout LFS objects | |
| run: git lfs checkout | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| $CONDA/bin/conda install -y -c bioconda womtool | |
| $CONDA/bin/conda config --add channels conda-forge | |
| $CONDA/bin/conda install -y -c conda-forge miniwdl shellcheck | |
| echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Test with tox | |
| run: tox | |
| # Send Slack message on workflow failure | |
| - name: Slack Failure Notification | |
| if: failure() | |
| uses: rtCamp/[email protected] | |
| env: | |
| SLACK_COLOR: '#DF5A49' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| SLACK_ICON: https://github.com/broadinstitute/long-read-pipelines/blob/main/.github/workflows/dnabad.png?raw=true | |
| SLACK_USERNAME: long-read-pipelines | |
| # Run WDL tests on self-hosted runner | |
| branch_test: | |
| needs: tox_test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Continuous integration test suite | |
| run: | | |
| echo 'Test temporarily disabled.' | |
| # Send Slack message on workflow failure | |
| - name: Slack Failure Notification | |
| if: failure() | |
| uses: rtCamp/[email protected] | |
| env: | |
| SLACK_COLOR: '#DF5A49' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| SLACK_ICON: https://github.com/broadinstitute/long-read-pipelines/blob/main/.github/workflows/dnabad.png?raw=true | |
| SLACK_USERNAME: long-read-pipelines | |
| # Send Slack message on workflow success | |
| - name: Slack Success Notification | |
| if: success() | |
| uses: rtCamp/[email protected] | |
| env: | |
| SLACK_COLOR: '#50D9C9' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| SLACK_ICON: https://github.com/broadinstitute/long-read-pipelines/blob/main/.github/workflows/dnagood.png?raw=true | |
| SLACK_USERNAME: long-read-pipelines |