c3c073e964
Fix stage_data.nf: use synthea:cudf container, Python-based downloads with sshpass/expect fallback
2026-04-01 10:03:56 +01:00
4b9152cf3c
Fix stage_data.nf: use ubuntu container with apt-get, create dirs on PVC
2026-04-01 09:30:00 +01:00
d1c471fa2a
Add stage_data.nf to download large files directly to PVC from alien server
2026-04-01 09:10:53 +01:00
9c26a6e49c
Debug PVC: check mounts and dir contents
2026-03-27 10:15:13 +01:00
83a79287b2
Simplified PVC debug script
2026-03-27 10:06:02 +01:00
de44607dc4
Switch reassemble container to synthea:cudf (known working)
2026-03-26 19:37:19 +01:00
45b634acf0
Fix reassemble.nf: use find to discover _parts dirs dynamically
2026-03-26 19:33:44 +01:00
983a2c3246
Add debug_pvc.nf to inspect PVC contents
2026-03-26 19:27:11 +01:00
bb11c598a0
Fix reassemble.nf: use Harbor-hosted container image
2026-03-26 18:32:03 +01:00
cf6968d0c6
Fix reassemble.nf: remove executor local so it runs on k8s with PVC access
2026-03-26 18:28:42 +01:00
88627edc25
Configure pipeline for WES execution on k8s cluster
...
- Add main.nf as WES entry point with PVC-based paths
- Update nextflow.config with k8s/k8s_gpu profiles (eureka-pvc)
- Update params.json defaults to /omic/eureka/digital-patients/ paths
- Remove stageInMode 'copy' from corto and vcf2prot for k8s compat
- Add reassemble.nf for one-time chunk reassembly on PVC
2026-03-26 17:58:28 +01:00
9e6a16c19b
Initial commit: digital-patients pipeline (clean, no large files)
...
Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.
2026-03-26 15:15:23 +01:00
