omic/synthea-alldiseases
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67bd6692b0a6641478dacc1da5d9c6ab39df282b
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7 Commits

Author SHA1 Message Date
Olamide Isreal
67bd6692b0 Clean up pipeline files 
- Remove unused variable and redundant comments/echo statements in main.nf
- Remove obsolete files: simple.nf, test.nf, generate_patients.sh,
  test_synthea.sh, trace.txt, docker-compose.yml
  (all referenced local-only synthea-module-generator image)
 2026-03-25 15:09:07 +01:00
Olamide Isreal
f8df39d9af Fix script to write outputs to Nextflow work dir 
- 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
 2026-03-25 14:51:09 +01:00
Olamide Isreal
02d93f9360 Fix image pull and gender arg for WES 
- 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
 2026-03-25 14:29:59 +01:00
Olamide Isreal
f29323323b Use pre-built jar and v2 tag to bypass Gradle permission issue 
- 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
 2026-03-25 13:30:24 +01:00
Olamide Isreal
d468509ec3 Configure synthea-alldiseases for WES execution 
- 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
 2026-03-25 12:31:34 +01:00
olamide24
e10ae0cf81 Fixed patient generation with separate script approach 2025-03-27 11:26:33 -07:00
Gabe Richman
2141e81f42 Trying to fix basic functionality again. 2025-03-23 11:53:47 -07:00