omic
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  • Joined on 2025-10-06
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omic pushed to main at omic/digital-patients 2026-04-01 09:46:39 +00:00
4db4b2ac06 Debug stage_data.nf: test PVC access, sshpass install, and network connectivity
omic pushed to main at omic/digital-patients 2026-04-01 09:27:52 +00:00
8695fa01e9 Fix stage_data.nf: pure bash with conda install sshpass, set +e to avoid early exit
omic pushed to main at omic/digital-patients 2026-04-01 09:04:08 +00:00
c3c073e964 Fix stage_data.nf: use synthea:cudf container, Python-based downloads with sshpass/expect fallback
omic pushed to main at omic/digital-patients 2026-04-01 08:30:12 +00:00
4b9152cf3c Fix stage_data.nf: use ubuntu container with apt-get, create dirs on PVC
omic pushed to main at omic/digital-patients 2026-04-01 08:11:06 +00:00
d1c471fa2a Add stage_data.nf to download large files directly to PVC from alien server
omic pushed to master at omic/foldseek 2026-03-30 20:18:22 +00:00
704f048c59 Reduce resource requirements to 2 cpus / 8GB memory for k8s compatibility
omic pushed to master at omic/foldseek 2026-03-30 19:54:15 +00:00
bf04f8971e Configure foldseek pipeline for WES execution
omic pushed to master at omic/foldseek 2026-03-30 18:21:38 +00:00
ec54fa1c22 Initialize foldseek pipeline for WES
omic created branch master in omic/foldseek 2026-03-30 18:21:38 +00:00
omic created repository omic/foldseek 2026-03-30 18:13:22 +00:00
omic pushed to main at omic/digital-patients 2026-03-27 09:15:25 +00:00
9c26a6e49c Debug PVC: check mounts and dir contents
omic pushed to main at omic/digital-patients 2026-03-27 09:06:15 +00:00
83a79287b2 Simplified PVC debug script
omic pushed to main at omic/digital-patients 2026-03-26 18:37:26 +00:00
de44607dc4 Switch reassemble container to synthea:cudf (known working)
omic pushed to main at omic/digital-patients 2026-03-26 18:33:53 +00:00
45b634acf0 Fix reassemble.nf: use find to discover _parts dirs dynamically
omic pushed to main at omic/digital-patients 2026-03-26 18:27:20 +00:00
983a2c3246 Add debug_pvc.nf to inspect PVC contents
omic pushed to main at omic/digital-patients 2026-03-26 17:32:11 +00:00
bb11c598a0 Fix reassemble.nf: use Harbor-hosted container image
omic pushed to main at omic/digital-patients 2026-03-26 17:28:51 +00:00
cf6968d0c6 Fix reassemble.nf: remove executor local so it runs on k8s with PVC access
omic pushed to main at omic/digital-patients 2026-03-26 17:10:04 +00:00
88627edc25 Configure pipeline for WES execution on k8s cluster
omic pushed to master at omic/bioemu 2026-03-26 16:46:48 +00:00
4cd23d549b Fix HOME env for colabfold weight download, increase resources, use v3 tag
omic pushed to master at omic/bioemu 2026-03-26 15:14:57 +00:00
844d34c04a Use bioemu:v2 tag to force k8s to pull fixed image with UID 1000 user