testing pr - Np jw test illumina genotyping arrays #184
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| name: Test Illumina Genotyping Array | |
| # Workflow triggers | |
| on: | |
| pull_request: | |
| branches: [ "develop", "staging", "master" ] | |
| paths: | |
| - 'pipelines/broad/genotyping/illumina/**' | |
| - 'tasks/**' | |
| - 'verification/**' | |
| - '.github/workflows/test_illumina_genotyping_array.yml' | |
| workflow_dispatch: | |
| inputs: | |
| useCallCache: | |
| description: 'Use call cache (default: true)' | |
| required: false | |
| default: "true" | |
| updateTruth: | |
| description: 'Update truth files (default: false)' | |
| required: false | |
| default: "false" | |
| env: | |
| PROJECT_NAME: WARP | |
| REPOSITORY_NAME: ${{ github.event.repository.name }} | |
| jobs: | |
| run_pipeline: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: 'read' | |
| id-token: 'write' | |
| steps: | |
| - uses: 'actions/checkout@v3' | |
| - name: Check working directory | |
| run: | | |
| echo "Current working directory:" | |
| pwd | |
| echo "Listing files in the working directory:" | |
| ls -alh | |
| - id: 'auth' | |
| name: 'Authenticate to Google Cloud' | |
| uses: 'google-github-actions/auth@v2' | |
| with: | |
| token_format: 'access_token' | |
| workload_identity_provider: 'projects/1038484894585/locations/global/workloadIdentityPools/github-wi-pool/providers/github-wi-provider' | |
| service_account: '[email protected]' | |
| access_token_lifetime: '3600' | |
| access_token_scopes: 'profile, email, openid' | |
| - name: Submit job, poll status, and get outputs | |
| id: pipeline_run | |
| run: | | |
| TOKEN="${{ steps.auth.outputs.access_token }}" | |
| NAMESPACE="warp-pipelines" | |
| WORKSPACE="WARP Tests" | |
| USE_CALL_CACHE="${{ github.event.inputs.useCallCache }}" | |
| UPDATE_TRUTH="${{ github.event.inputs.updateTruth }}" | |
| TEST_TYPE="Plumbing" | |
| CURRENT_TIME=$(date +"%Y-%m-%d-%H-%M-%S") | |
| PIPELINE_NAME="IlluminaGenotypingArray" | |
| PIPELINE_DIR="pipelines/broad/genotyping/illumina" | |
| TRUTH_PATH="gs://broad-warp-test-storage/illumina_genotyping_array/truth" | |
| RESULTS_PATH="gs://broad-warp-test-storage/illumina_genotyping_array/results/$CURRENT_TIME" | |
| # Create JSON for submission data | |
| SUBMISSION_DATA_FILE="submission_data.json" | |
| CALL_CACHE_VALUE="true" | |
| if [ "$USE_CALL_CACHE" = "false" ]; then | |
| CALL_CACHE_VALUE="false" | |
| fi | |
| if [ "$UPDATE_TRUTH" = "true" ]; then | |
| UPDATE_TRUTH=true | |
| else | |
| UPDATE_TRUTH=false | |
| fi | |
| cat <<EOF > "$SUBMISSION_DATA_FILE" | |
| { | |
| "methodConfigurationNamespace": "warp-pipelines", | |
| "methodConfigurationName": "$PIPELINE_NAME", | |
| "useCallCache": $CALL_CACHE_VALUE, | |
| "deleteIntermediateOutputFiles": false, | |
| "useReferenceDisks": true, | |
| "memoryRetryMultiplier": 1.2, | |
| "workflowFailureMode": "NoNewCalls", | |
| "userComment": "Automated submission", | |
| "ignoreEmptyOutputs": false | |
| } | |
| EOF | |
| INPUTS_DIR=$PIPELINE_DIR/test_inputs/$TEST_TYPE | |
| for input_file in $INPUTS_DIR/*; do | |
| test_input_file=$(python3 scripts/firecloud_api/UpdateTestInputs.py \ | |
| --truth_path $TRUTH_PATH \ | |
| --results_path $RESULTS_PATH \ | |
| --inputs_json $input_file \ | |
| --update_truth $UPDATE_TRUTH) | |
| # Removed the following lines: | |
| # python3 scripts/firecloud_api/firecloud_api.py \ | |
| # --token "$TOKEN" \ | |
| # --namespace "$NAMESPACE" \ | |
| # --workspace "$WORKSPACE" \ | |
| # --action upload_file \ | |
| # --pipeline_name "$PIPELINE_NAME" \ | |
| # --test_input_file "$test_input_file" | |
| SUBMISSION_ID=$(python3 scripts/firecloud_api/firecloud_api.py \ | |
| --token "$TOKEN" \ | |
| --namespace "$NAMESPACE" \ | |
| --workspace "$WORKSPACE" \ | |
| --action submit \ | |
| --submission_data_file "$SUBMISSION_DATA_FILE") | |
| if [ -z "$SUBMISSION_ID" ]; then | |
| echo "Submission failed for input: $input_file" | |
| continue | |
| fi | |
| echo "Submission ID for input $input_file: $SUBMISSION_ID" | |
| RESPONSE=$(python3 scripts/firecloud_api/firecloud_api.py \ | |
| --token "$TOKEN" \ | |
| --namespace "$NAMESPACE" \ | |
| --workspace "$WORKSPACE" \ | |
| --action poll_status \ | |
| --submission_id "$SUBMISSION_ID") | |
| echo "Workflows for input $input_file and their statuses:" | |
| echo "$RESPONSE" | jq | |
| for WORKFLOW_ID in $(echo "$RESPONSE" | jq -r 'keys[]'); do | |
| OUTPUT=$(python3 scripts/firecloud_api/firecloud_api.py \ | |
| --token "$TOKEN" \ | |
| --namespace "$NAMESPACE" \ | |
| --workspace "$WORKSPACE" \ | |
| --action get_outputs \ | |
| --submission_id "$SUBMISSION_ID" \ | |
| --workflow_id "$WORKFLOW_ID" \ | |
| --pipeline_name "$PIPELINE_NAME") | |
| echo "Output for workflow $WORKFLOW_ID: $OUTPUT" | |
| done | |
| done | |