run-pipelines #50
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
| name: seqera-showcase-autotest-staging | |
| run-name: run-pipelines | |
| # Triggers workflow runs on demand, with schedule, or on push. | |
| # workflow_dispatch: Manually trigger workflow from Actions tab. | |
| # dryrun: Whether to do a dry run without submitting pipeline. | |
| # timer: Delay before starting run. | |
| # slack: Notify Slack on run completion. | |
| # remove/force: Cleanup run after completion. | |
| # schedule: Cron schedule to trigger runs automatically. | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| dryrun: | |
| description: "Dryrun (do not submit pipeline)" | |
| default: false | |
| type: boolean | |
| required: false | |
| timer: | |
| description: "Environment" | |
| default: delay60mins | |
| type: choice | |
| options: | |
| - noDelay | |
| - delay1mins | |
| - delay5mins | |
| - delay15mins | |
| - delay30mins | |
| - delay60mins | |
| - delay120mins | |
| - delay360mins | |
| - delay720mins | |
| - waitForReviewer | |
| slack: | |
| description: Slack hook | |
| type: boolean | |
| required: false | |
| default: true | |
| remove: | |
| description: Delete run | |
| default: true | |
| type: boolean | |
| required: false | |
| force: | |
| description: Force delete run | |
| default: false | |
| type: boolean | |
| required: false | |
| pre_run: | |
| description: Pre-run command | |
| default: "" | |
| type: string | |
| required: false | |
| config: | |
| description: Nextflow config to add | |
| default: "" | |
| type: string | |
| required: false | |
| launch_container: | |
| description: The container to be used to run Nextflow head job | |
| default: "" | |
| type: string | |
| required: false | |
| # schedule: | |
| # # Every 2am | |
| # - cron: "0 2 * * *" | |
| env: | |
| TOWER_API_ENDPOINT: ${{ secrets.STAGING_TOWER_ACCESS_ENDPOINT }} | |
| # This workflow launches pipelines in Tower, waits for completion, | |
| # extracts metadata, and optionally sends Slack notifications. | |
| # The 'launch' job runs the launch_pipelines.py script to start the | |
| # pipelines. It uploads the Tower launch data as an artifact. | |
| # The 'clearup-and-delete' job downloads the artifact, runs | |
| # extract_metadata.py to collect metadata, sends Slack notifications | |
| # if configured, and deletes the workflow run if configured. | |
| jobs: | |
| launch: | |
| runs-on: ubuntu-latest | |
| env: | |
| TOWER_ACCESS_TOKEN: ${{ secrets.STAGING_TOWER_ACCESS_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: setup python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" | |
| - name: install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| - name: install tw cli | |
| run: | | |
| set -euo pipefail | |
| wget -L https://github.com/seqeralabs/tower-cli/releases/download/v0.10.1/tw-linux-x86_64 | |
| mv tw-* tw | |
| chmod +x tw | |
| sudo mv tw /usr/local/bin/ | |
| - name: tower check | |
| run: | | |
| tw --version | |
| - name: launch_pipelines | |
| run: | | |
| python launch_pipelines.py \ | |
| -l DEBUG \ | |
| -i \ | |
| pipelines/staging*.yaml \ | |
| compute-envs/staging*.yaml \ | |
| ${{ (github.event_name == 'workflow_dispatch' && inputs.pre_run != '') && format('--pre_run "{0}"', inputs.pre_run) || ''}} \ | |
| ${{ (github.event_name == 'workflow_dispatch' && inputs.config != '') && format('--config "{0}"', inputs.config) || '' }} \ | |
| ${{ (github.event_name == 'workflow_dispatch' && inputs.launch_container) && format('--launch-container "{0}"', inputs.launch_container) || '' }} \ | |
| ${{ (github.event_name == 'workflow_dispatch' && inputs.dryrun == 'true') && '--dryrun' || '' }} \ | |
| -o ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}.json | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_launch_json | |
| path: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}.json | |
| clearup-and-delete: | |
| runs-on: ubuntu-latest | |
| needs: [launch] | |
| environment: ${{ inputs.timer || 'delay60mins' }} | |
| env: | |
| TOWER_ACCESS_TOKEN: ${{ secrets.STAGING_TOWER_ACCESS_TOKEN }} | |
| SLACK_BOT_TOKEN: ${{ secrets.SLACK_BOT_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/download-artifact@v3 | |
| with: | |
| name: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_launch_json | |
| path: run_details | |
| - name: Install tw CLI | |
| run: | | |
| set -euo pipefail | |
| wget -L https://github.com/seqeralabs/tower-cli/releases/download/v0.9.2/tw-linux-x86_64 | |
| mv tw-* tw | |
| chmod +x tw | |
| sudo mv tw /usr/local/bin/ | |
| - name: tower check | |
| run: | | |
| tw --version | |
| - name: setup python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| cache: "pip" | |
| - name: install dependencies | |
| run: | | |
| pip install -r requirements.txt | |
| - name: finish workflow | |
| run: | | |
| python extract_metadata.py \ | |
| -l DEBUG \ | |
| -o ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_workflow_data.json \ | |
| -i run_details/* \ | |
| --slack_channel ${{ secrets.SLACK_CHANNEL }} \ | |
| ${{ ( github.event_name != 'workflow_dispatch' || inputs.slack == 'true' ) && '--slack' || '' }} \ | |
| ${{ ( github.event_name != 'workflow_dispatch' || inputs.remove == 'true' ) && '--delete' || '' }} \ | |
| ${{ ( github.event_name != 'workflow_dispatch' || inputs.force == 'true' ) && '--force' || '' }} | |
| - uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_workflow_data | |
| path: ${{ github.run_id }}_${{ github.run_number }}_${{ github.run_attempt }}_workflow_data.json |