Bumped nextflow to 24.04.2 and enforced min version through config #57
Workflow file for this run
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| name: Main branch Build and Deployment | |
| on: | |
| pull_request: | |
| types: [closed] | |
| branches: | |
| - main | |
| jobs: | |
| on-merge-and-deploy: | |
| name: Skip on unmerged or 'no-deploy' PRs | |
| if: github.event.pull_request.merged == true && !contains(github.event.pull_request.labels.*.name, 'no-deploy') | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Confirm execution | |
| shell: bash | |
| run: | | |
| echo "PR merge detected and deployment wanted." | |
| pipeline-deploy-aws-infra: | |
| name: Deploy/update AWS infrastructure for pipeline | |
| needs: [on-merge-and-deploy] | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: pipeline/aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: Setup node.js (CDK requirement) | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "18" | |
| - name: Install CDK | |
| run: npm install -g aws-cdk | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install CDK stack dependencies | |
| run: pip install -r requirements.txt | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-deploy | |
| aws-region: us-east-1 | |
| - name: CDK validations (resource assertions and cdk diff) | |
| run: make validate | |
| - name: cdk deploy | |
| run: make deploy ADD_CDK_ARGS="--require-approval never" | |
| api-deploy-image-repo: | |
| name: Deploy/update container image repository stack for API | |
| needs: [on-merge-and-deploy] | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: api/aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: Setup node.js (CDK requirement) | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "18" | |
| - name: Install CDK | |
| run: npm install -g aws-cdk | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install CDK stack dependencies | |
| run: pip install -r requirements.txt | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-cdk-deploy | |
| aws-region: us-east-1 | |
| - name: CDK validations (resource assertions and cdk diff) | |
| run: make validate-image-stack | |
| - name: cdk deploy | |
| run: cdk deploy PaviApiImageRepoCdkStack --require-approval never | |
| pipeline-seq-retrieval-build-and-push-docker-image: | |
| needs: [on-merge-and-deploy, pipeline-deploy-aws-infra] | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/seq_retrieval/ | |
| - name: Store release tag in env | |
| shell: bash | |
| run: | | |
| echo "tagname=$(git describe --tags)" >> $GITHUB_ENV | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-build-image-pipeline-seq-retrieval | |
| aws-region: us-east-1 | |
| - name: Amazon ECR login | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| - name: Build and push container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/seq_retrieval/ | |
| push: true | |
| tags: | | |
| ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{ env.tagname }} | |
| ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_seq_retrieval:${{ github.event.pull_request.base.ref }} | |
| platforms: linux/amd64 | |
| pipeline-alignment-build-and-push-docker-image: | |
| needs: [on-merge-and-deploy, pipeline-deploy-aws-infra] | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| pipeline/alignment/ | |
| - name: Store release tag in env | |
| shell: bash | |
| run: | | |
| echo "tagname=$(git describe --tags)" >> $GITHUB_ENV | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-build-image-pipeline-seq-retrieval | |
| aws-region: us-east-1 | |
| - name: Amazon ECR login | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| - name: Build and push container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./pipeline/alignment/ | |
| push: true | |
| tags: | | |
| ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{ env.tagname }} | |
| ${{ steps.login-ecr.outputs.registry }}/agr_pavi/pipeline_alignment:${{ github.event.pull_request.base.ref }} | |
| platforms: linux/amd64 | |
| api-build-and-push-docker-image: | |
| needs: [on-merge-and-deploy, api-deploy-image-repo] | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Store release tag in env | |
| shell: bash | |
| run: | | |
| echo "tagname=$(git describe --tags)" >> $GITHUB_ENV | |
| # This step will configure environment variables to be used by all steps | |
| # involving AWS interaction further down | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-build-image-pipeline-seq-retrieval | |
| aws-region: us-east-1 | |
| - name: Amazon ECR login | |
| id: login-ecr | |
| uses: aws-actions/amazon-ecr-login@v2 | |
| - name: Build and push container image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./ | |
| file: api/Dockerfile | |
| push: true | |
| tags: | | |
| ${{ steps.login-ecr.outputs.registry }}/agr_pavi/api:${{ env.tagname }} | |
| ${{ steps.login-ecr.outputs.registry }}/agr_pavi/api:${{ github.event.pull_request.base.ref }} | |
| platforms: linux/amd64 | |
| api-deploy-application: | |
| name: Deploy application (version) for API | |
| needs: | |
| - on-merge-and-deploy | |
| - api-build-and-push-docker-image | |
| - pipeline-alignment-build-and-push-docker-image | |
| - pipeline-seq-retrieval-build-and-push-docker-image | |
| permissions: | |
| id-token: write # This is required for requesting the JWT for gaining permissions to assume the IAM role to perform AWS actions | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| working-directory: api/aws_infra | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Store release tag in env | |
| shell: bash | |
| run: | | |
| echo "tagname=$(git describe --tags)" >> $GITHUB_ENV | |
| - name: Setup node.js (CDK requirement) | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "18" | |
| - name: Install CDK | |
| run: npm install -g aws-cdk | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Install CDK stack dependencies | |
| run: pip install -r requirements.txt | |
| - name: AWS credentials configuration | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: ${{secrets.GH_ACTIONS_AWS_ROLE}} | |
| role-session-name: gh-actions-${{github.run_id}}.${{github.run_number}}.${{github.run_attempt}}-api-cdk-deploy | |
| aws-region: us-east-1 | |
| - name: CDK validations (resource assertions and cdk diff) | |
| run: make validate-application-stack validate-environment-stack | |
| - name: Deploy application (and version) | |
| run: make deploy-application PAVI_DEPLOY_VERSION_LABEL="${{ env.tagname }}" ADD_CDK_ARGS="--require-approval never" | |
| - name: Deploy to main environment | |
| run: make deploy-environment PAVI_DEPLOY_VERSION_LABEL="${{ env.tagname }}" PAVI_IMAGE_TAG="${{ env.tagname }}" \ | |
| DEPLOY_ENVIRONMENT=PaviApiEbMainStack ADD_CDK_ARGS="--require-approval never" |