Bugfix: remove unecessary parameter in se_to_pe_fastq test #150
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| name: Build Docker images and test pipeline | |
| on: | |
| push: | |
| jobs: | |
| build-docker: | |
| strategy: | |
| matrix: | |
| IMAGE_NAME: ['microc', 'microc_qc', 'rcmc', 'juicer', 'cooler', 'seqkit', 'utils'] | |
| name: Build Docker | |
| runs-on: ubuntu-latest | |
| # Add "id-token" with the intended permissions. | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| # Configure Workload Identity Federation and generate an access token. | |
| - id: 'auth' | |
| name: 'Authenticate to Google Cloud' | |
| uses: 'google-github-actions/auth@v0' | |
| with: | |
| workload_identity_provider: 'projects/303574531351/locations/global/workloadIdentityPools/github-actions-pool/providers/github-provider' | |
| service_account: 'github-actions@aryeelab.iam.gserviceaccount.com' | |
| # Setup gcloud CLI | |
| - name: Set up Cloud SDK | |
| uses: google-github-actions/setup-gcloud@v0 | |
| # Build and push image to Google Container Registry | |
| - name: Build | |
| run: |- | |
| GIT_TAG=$(git describe --tags) | |
| gcloud builds submit \ | |
| --config Docker/cloudbuild.yaml \ | |
| --region=us-central1 \ | |
| --substitutions _GIT_TAG=$GIT_TAG,_IMAGE_NAME=${{ matrix.IMAGE_NAME }} | |
| test-pipelines: | |
| name: Test Pipelines | |
| needs: build-docker | |
| runs-on: ubuntu-latest | |
| # Add "id-token" with the intended permissions. | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Change docker version from latest to current git commit tag (if version is dev) | |
| run: | | |
| GIT_TAG=$(git describe --tags) | |
| echo Replacing 'dev' with $GIT_TAG if necessary | |
| sed -i "s/String pipeline_ver = 'dev'/String pipeline_ver = '$GIT_TAG'/" microc.wdl | |
| echo Confirming version in microc.wdl: | |
| cat microc.wdl | grep "String pipeline_ver =" | |
| - name: Install pytest-worfklow and Cromwell dependencies | |
| run: | | |
| pip install pytest-workflow | |
| wget -nv https://github.com/broadinstitute/cromwell/releases/download/80/cromwell-80.jar | |
| echo '#!/bin/bash' > /usr/local/bin/cromwell | |
| echo exec \"${JAVA_HOME}/bin/java\" $JAVA_OPTS -jar \"${PWD}/cromwell-80.jar\" '"$@"' >> /usr/local/bin/cromwell | |
| cat /usr/local/bin/cromwell | |
| chmod +x /usr/local/bin/cromwell | |
| - id: 'auth' | |
| name: 'Authenticate to Google Cloud' | |
| uses: 'google-github-actions/auth@v0' | |
| with: | |
| token_format: 'access_token' | |
| workload_identity_provider: 'projects/303574531351/locations/global/workloadIdentityPools/github-actions-pool/providers/github-provider' | |
| service_account: 'github-actions@aryeelab.iam.gserviceaccount.com' | |
| - id: 'docker-login' | |
| name: 'Docker login to Artifact Registry' | |
| uses: 'docker/login-action@v1' | |
| with: | |
| registry: 'us-central1-docker.pkg.dev' | |
| username: 'oauth2accesstoken' | |
| password: '${{ steps.auth.outputs.access_token }}' | |
| - name: Run tests | |
| run: | | |
| pytest --keep-workflow-wd --basetemp /tmp/pytest_workflow | |
| - name: Run pipeline to get full cromwell logs if pytest fails | |
| if: ${{ failure() }} | |
| run: | | |
| cromwell run -i tests/small-region-capture-micro-c/small_rcmc.json microc.wdl | |
| - name: Upload cromwell logs to GCP bucket | |
| if: ${{ failure() }} | |
| run: | | |
| GIT_TAG=$(git describe --tags) | |
| LOG_TGZ=$(date +"%Y-%m-%d")-cromwell-executions-${GIT_TAG}.tgz | |
| tar cfv $LOG_TGZ /home/runner/work/topology-tools/topology-tools/cromwell-executions | |
| gsutil cp $LOG_TGZ gs://aryeelab-github-actions-logs/ | |
| - name: Show pytest logs | |
| run: | | |
| echo "STDOUT:" | |
| cat /tmp/pytest_workflow/*/log.out | |
| echo "STDERR:" | |
| cat /tmp/pytest_workflow/*/log.err |