Merge pull request #93 from AlexsLemonade/jashapiro/92-nextflow-resume #38
Workflow file for this run
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| name: Run Workflow on AWS Batch | |
| on: | |
| push: | |
| tags: | |
| - "v*.*.*" | |
| - "[0-9]+-[0-9]+-[0-9]+" | |
| workflow_dispatch: | |
| inputs: | |
| revision: | |
| description: Branch or tag of workflow to run | |
| required: true | |
| default: main | |
| data_release: | |
| description: Data release date | |
| required: true | |
| default: default | |
| run_mode: | |
| description: Workflow run mode | |
| type: choice | |
| options: | |
| - test | |
| - simulated | |
| - scpca | |
| - full | |
| output_mode: | |
| description: Workflow output mode | |
| type: choice | |
| default: staging | |
| options: | |
| - staging | |
| - prod | |
| resume: | |
| description: Use -resume flag for Nextflow launch | |
| type: boolean | |
| default: true | |
| permissions: | |
| id-token: write # This is required for requesting the JWT | |
| contents: read # This is required for actions/checkout | |
| jobs: | |
| build: | |
| name: Run Code Deploy Job | |
| runs-on: ubuntu-latest | |
| environment: "prod" | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v4 | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::992382809252:role/GithubOpenId-nextflow | |
| role-session-name: githubActionSession | |
| aws-region: us-east-1 | |
| - name: Create tmux launch script | |
| env: | |
| # use the github tag if a push event, or the workflow input if a manual trigger | |
| revision: ${{ github.event_name == 'push' && github.ref_name || inputs.revision }} | |
| # default data release for release events specified, otherwise use the specified data release | |
| data_release: ${{ github.event_name == 'push' && 'default' || inputs.data_release }} | |
| # default run mode is full for release events, otherwise use the specified mode | |
| run_mode: ${{ github.event_name == 'push' && 'full' || inputs.run_mode }} | |
| # default output mode is prod for release events, otherwise use the specified mode | |
| output_mode: ${{ github.event_name == 'push' && 'prod' || inputs.output_mode }} | |
| resume: ${{ github.event_name == 'push' && 'true' || inputs.resume }} | |
| run: | | |
| echo '#!/bin/bash' > scripts/tmux_launch.sh | |
| echo "export GITHUB_TAG=$revision" >> scripts/tmux_launch.sh | |
| echo "export DATA_RELEASE=$data_release" >> scripts/tmux_launch.sh | |
| echo "export RUN_MODE=$run_mode" >> scripts/tmux_launch.sh | |
| echo "export OUTPUT_MODE=$output_mode" >> scripts/tmux_launch.sh | |
| echo "export RESUME=$resume" >> scripts/tmux_launch.sh | |
| echo 'tmux new-session -d -s nextflow /opt/nextflow/scripts/run_nextflow.sh' >> scripts/tmux_launch.sh | |
| chmod +x scripts/tmux_launch.sh | |
| - name: Create zip archive | |
| run: | | |
| zip -r source.zip . -i appspec.yml LICENSE scripts/** | |
| working-directory: ${{ github.workspace }} | |
| - name: Copy zip to S3 | |
| run: aws s3 cp source.zip s3://pipeline-artifact-992382809252-us-east-2/ | |
| env: | |
| AWS_DEFAULT_REGION: us-east-2 | |
| - name: Trigger AWS CodeDeploy deployment | |
| run: | | |
| aws deploy create-deployment \ | |
| --application-name Batch \ | |
| --deployment-group-name Batch-deployment-group \ | |
| --s3-location bucket=pipeline-artifact-992382809252-us-east-2,key=source.zip,bundleType=zip \ | |
| --region us-east-2 | |
| env: | |
| AWS_DEFAULT_REGION: us-east-2 |