- Save pwd before cd /app so outputs go to correct location
- Use set +e and PIPESTATUS to handle java exit code gracefully
- Exit 0 if FHIR files were generated successfully
- Push as Docker V2 manifest (no OCI index/attestation) so K8s can pull
- Tag as v3 to avoid cached image issues
- Fix gender: omit -g flag for 0.5 (both), Synthea only accepts M or F
- Call java -jar synthea-with-dependencies.jar directly instead of
run_synthea which invokes Gradle at runtime
- Tag image as v2 to force K8s to pull fresh image
- Rewrite params.json to match WES tool registry format
- Update main.nf to use Harbor container image
- Add k8s profile to nextflow.config for WES/Kubernetes execution
- Use s3://omic/eureka paths for output
