Added RemoveSingleOrganismContamination to dockstore. (#500) #227
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| # Continuous integration and delivery of the main branch. | |
| name: CI/CD | |
| on: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| # Run Python tests on Github runner | |
| tox_test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.13] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Setup Environment | |
| uses: ./.github/actions/setup-environment # Path to your composite action | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| conda-python-version: '3.12' # Keep this specific if miniwdl needs 3.12 | |
| - name: Test with tox | |
| run: tox | |
| # Send Slack message on workflow failure | |
| - name: Slack Failure Notification | |
| if: failure() | |
| uses: rtCamp/action-slack-notify@v2.0.2 | |
| 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 | |
| main_test: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| # Runs a set of commands using the runners shell | |
| - name: Continuous integration test suite | |
| run: | | |
| echo 'Test temporarily disabled.' | |
| # Send Slack message on workflow failure | |
| - name: Slack Failure Notification | |
| if: failure() | |
| uses: rtCamp/action-slack-notify@v2.0.2 | |
| 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/action-slack-notify@v2.0.2 | |
| 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 | |
| deliver: | |
| # Automatic delivery will run on a Github-hosted machine | |
| needs: main_test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: Read Current Version | |
| id: read_property | |
| uses: christian-draeger/read-properties@1.0.0 | |
| with: | |
| path: 'VERSION' | |
| property: 'version' | |
| - name: Current Version | |
| run: echo ${{ steps.read_property.outputs.value }} | |
| - name: Generate Release Notes | |
| # Retrieves the commit message from the last commit in current branch (main) | |
| # and writes it to a file called release_notes.txt | |
| run: git log --format=%B -n 1 ${{ github.event.after }} > release_notes.txt | |
| - name: Github Bumpversion Action | |
| id: version-bump | |
| uses: jasonamyers/github-bumpversion-action@v1.0.4 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| DEFAULT_BUMP: "patch" | |
| - name: New Version | |
| run: echo ${{ steps.version-bump.outputs.new_ver }} | |
| - name: Push Changes To Master/Main | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| tags: true | |
| - name: Create Github release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: ${{ steps.version-bump.outputs.new_ver }} | |
| release_name: 'lrp_${{ steps.version-bump.outputs.new_ver }}' | |
| body_path: "release_notes.txt" | |
| draft: false | |
| prerelease: false | |
| - name: Slack Failure Notification | |
| if: failure() | |
| uses: rtCamp/action-slack-notify@v2.0.2 | |
| env: | |
| SLACK_MESSAGE: 'Failed to release version lrp_${{ steps.bump_version.outputs.next-version }}' | |
| SLACK_COLOR: '#DF5A49' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| SLACK_ICON: https://github.com/broadinstitute/long-read-pipelines/blob/main/.github/workflows/dnabad.png?raw=true | |
| SLACK_USERNAME: long-read-pipelines | |
| - name: Slack Success Notification | |
| if: success() | |
| uses: rtCamp/action-slack-notify@v2.0.2 | |
| env: | |
| SLACK_MESSAGE: 'Successfully released version lrp_${{ steps.bump_version.outputs.next-version }}' | |
| 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 |