diff --git a/.github/workflows/variant-calling-test-run.yml b/.github/workflows/variant-calling-test-run.yml index 8cd5612..0cf9a2a 100644 --- a/.github/workflows/variant-calling-test-run.yml +++ b/.github/workflows/variant-calling-test-run.yml @@ -238,25 +238,43 @@ jobs: # Create a directory for workflow logs mkdir -p workflow_logs - # Run workflow with more verbose logging + echo "=== Running Cromwell with test workflow ===" + # Run with more detailed logging and capture all output java -Dbackend.providers.Local.config.root="workflow_logs" \ - -Xmx4g -jar cromwell-86.jar run \ + -Dconfig.trace=true \ + -Dakka.loglevel=DEBUG \ + -Xmx4g \ + -jar cromwell-86.jar \ + run \ variantCalling/variantCalling.wdl \ --inputs test/test-inputs.json \ --metadata-output workflow_logs/metadata.json \ 2>&1 | tee workflow_logs/workflow.log - - # If workflow fails, print additional debug info + + # If workflow fails, print debug info if [ $? -ne 0 ]; then echo "=== Workflow failed, printing debug information ===" - echo "=== Last 50 lines of workflow log ===" - tail -n 50 workflow_logs/workflow.log - echo "=== Execution directory contents ===" - ls -R workflow_logs + echo "=== Directory contents ===" + ls -R workflow_logs/ + + echo "=== Last 100 lines of workflow log ===" + tail -n 100 workflow_logs/workflow.log + + echo "=== Contents of stderr files if they exist ===" + find workflow_logs -name "stderr" -type f -exec sh -c 'echo "=== File: {}"; cat {}' \; + + echo "=== Contents of stdout files if they exist ===" + find workflow_logs -name "stdout" -type f -exec sh -c 'echo "=== File: {}"; cat {}' \; + + echo "=== Contents of script files if they exist ===" + find workflow_logs -name "script" -type f -exec sh -c 'echo "=== File: {}"; cat {}' \; - # Print content of stderr from the failed task if it exists - find workflow_logs -name "stderr" -exec sh -c 'echo "=== Content of {}" && cat {}' \; + # Also print metadata if it exists + if [ -f workflow_logs/metadata.json ]; then + echo "=== Workflow metadata ===" + cat workflow_logs/metadata.json + fi # Exit with failure exit 1