run-pipelines #153
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| name: seqera-showcase-autotest-production | |
| 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: "https://api.cloud.seqera.io" | |
| # 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.TOWER_ACCESS_TOKEN }} | |
| PRE_RUN: ${{ github.event_name != 'workflow_dispatch' && 'true' || inputs.pre_run }} | |
| 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/production*.yaml \ | |
| compute-envs/production*.yaml \ | |
| include/*.yaml \ | |
| exclude/* \ | |
| ${{ (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.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 |