bump for even longer reads #5584
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |