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PR validation

Move to managed Nextflow AWS execution policy #79

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Move to managed Nextflow AWS execution policy

Move to managed Nextflow AWS execution policy #79

Workflow file for this run

.github/workflows/PR-validation.yml at 7e2104f
name: PR validation
on:
pull_request:
types: [synchronize, opened, reopened, edited]
branches:
- main
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
cancel-in-progress: true
jobs:
pipeline-seq-retrieval-container-image-build:
name: pipeline/seq_retrieval container-image build
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: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Build container image
uses: docker/build-push-action@v5
with:
context: ./pipeline/seq_retrieval/
push: false
tags: agr_pavi/pipeline_seq_retrieval:latest
outputs: type=docker,dest=/tmp/pavi_seq_retrieval_docker_image.tar
- name: Upload image as artifact (share between jobs)
uses: actions/upload-artifact@v4
with:
name: seq_retrieval_image
path: /tmp/pavi_seq_retrieval_docker_image.tar
pipeline-seq-retrieval-code-checks:
name: pipeline/seq_retrieval code checks
runs-on: ubuntu-22.04
defaults:
run:
shell: bash
working-directory: ./pipeline/seq_retrieval/
steps:
- name: Check out repository code
uses: actions/checkout@v4
with:
fetch-depth: 0
sparse-checkout: |
pipeline/seq_retrieval/
- uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Python typing test
run: |
make run-python-type-check
- name: Python style test
run: |
make run-python-style-check
- name: Run unit tests
run: |
make run-unit-tests
pipeline-alignment-container-image-build:
name: pipeline/alignment container-image build
runs-on: ubuntu-22.04
steps:
- name: Check out repository code
uses: actions/checkout@v4
with:
fetch-depth: 0
sparse-checkout: |
pipeline/alignment/
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Build container image
uses: docker/build-push-action@v5
with:
context: ./pipeline/alignment/
push: false
tags: agr_pavi/pipeline_alignment:latest
outputs: type=docker,dest=/tmp/pavi_alignment_docker_image.tar
- name: Upload image as artifact (share between jobs)
uses: actions/upload-artifact@v4
with:
name: alignment_image
path: /tmp/pavi_alignment_docker_image.tar
pipeline-alignment-unit-testing:
name: pipeline/alignment unit testing
needs:
- pipeline-alignment-container-image-build
runs-on: ubuntu-22.04
defaults:
run:
shell: bash
working-directory: ./pipeline/alignment/
steps:
- name: Check out repository code
uses: actions/checkout@v4
with:
fetch-depth: 0
sparse-checkout: |
pipeline/alignment/
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Download alignment image artifact (from previous job)
uses: actions/download-artifact@v4
with:
name: alignment_image
path: /tmp
- name: Load alignment Docker image
run: |
docker load --input /tmp/pavi_alignment_docker_image.tar
- name: Run unit test
run: |
make run-unit-tests
pipeline-workflow-integration-testing:
name: pipeline/workflow integration testing
needs:
- pipeline-seq-retrieval-container-image-build
- pipeline-alignment-container-image-build
runs-on: ubuntu-22.04
defaults:
run:
shell: bash
working-directory: ./pipeline/workflow/
steps:
- name: Check out repository code
uses: actions/checkout@v4
with:
fetch-depth: 0
sparse-checkout: |
pipeline/workflow/
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Download seq_retrieval image artifact (from previous job)
uses: actions/download-artifact@v4
with:
name: seq_retrieval_image
path: /tmp
- name: Download alignment image artifact (from previous job)
uses: actions/download-artifact@v4
with:
name: alignment_image
path: /tmp
- name: Load seq_retrieval Docker image
run: |
docker load --input /tmp/pavi_seq_retrieval_docker_image.tar
- name: Load alignment Docker image
run: |
docker load --input /tmp/pavi_alignment_docker_image.tar
- name: Run integration test
run: |
make run-integration-test
pipeline-aws-infra-code-checks:
name: pipeline/aws_infra code checks
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
with:
fetch-depth: 0
sparse-checkout: |
pipeline/aws_infra/
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: CDK resource assertions (unit tests)
run: |
make run-unit-tests
- name: Python typing test
run: |
make run-python-type-check
- name: Python style test
run: |
make run-python-style-check
- name: Setup node.js (CDK requirement)
uses: actions/setup-node@v4
with:
node-version: "18"
- name: Install CDK CLI
run: npm install -g aws-cdk
- 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-test
aws-region: us-east-1
- name: Validate production CDK stack code
run: cdk diff PaviPipelineCdkStack