omic/pocketminer
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12 Commits

Author SHA1 Message Date
Olamide Isreal
8e3b2170e9 Clean up pipeline configuration 
- Remove debug logging and dead PVC/direct-path fallbacks from main.nf
- Remove nf-amazon plugin and PVC storage config from nextflow.config
  (S3 access is handled by boto3 in the script)
- Simplify input download and output upload to single boto3 blocks
 2026-03-23 18:27:50 +01:00
Olamide Isreal
a430caaf96 Upload results to S3 via boto3 instead of publishDir (fixes S3 write) 2026-03-23 18:07:53 +01:00
Olamide Isreal
e52adef212 Use v2 image tag to force fresh pull with boto3 baked in 2026-03-23 17:56:16 +01:00
Olamide Isreal
9d132c308d Install boto3 at runtime for authenticated S3 download (fix syntax error) 2026-03-23 16:14:05 +01:00
Olamide Isreal
c0f0e38f27 Use boto3/signed URL for authenticated MinIO download (403 fix) 2026-03-23 16:06:50 +01:00
Olamide Isreal
7abd6eb267 Use wget/python instead of curl for MinIO download (curl not in image) 2026-03-23 15:56:09 +01:00
Olamide Isreal
e74a9441a4 Fix input resolution: disable bash strict mode, quiet logging, add auth fallback 2026-03-23 15:50:52 +01:00
Olamide Isreal
35dd4ab976 Add multi-method input file resolution for WES 
PVC mount is not available in k8s pods. Try multiple fallback
methods to retrieve input PDB: PVC path, s3-to-PVC conversion,
AWS CLI from MinIO, and curl from MinIO. Also add nf-amazon
plugin and s3:// default paths.
 2026-03-23 15:41:13 +01:00
Olamide Isreal
14091fce87 Match meta-predictor's working WES pattern 
- Add executor, docker, k8s storage config to k8s profile
- Use val input instead of file channel (avoids S3 staging issue)
- Pass PDB path as string, copy from PVC mount inside script
- Add PVC mount debug logging
- Set default params to /omic/eureka paths
 2026-03-23 15:27:23 +01:00
Olamide Isreal
4660bdf62a Remove stageInMode copy — may conflict with k8s executor 2026-03-23 14:04:50 +01:00
Olamide Isreal
5465d9b8b1 Fix nextflow.config to match WES k8s pattern 
- Match p2rank's working config structure: k8s profile only sets container
- Let WES-generated profile.config handle executor, storage, and k8s settings
- Add memory (8GB) and cpu (2) resource requests
- Set params defaults to null (values provided by WES experiment_params)
- Add manifest metadata
 2026-03-23 13:51:38 +01:00
Olamide Isreal
42d4e6cb87 Add WES pipeline configuration for pocketminer 
- Add Nextflow pipeline (main.nf) with Harbor container image
- Add nextflow.config with k8s/k8s_gpu/standard profiles
- Add params.json for TRS/WES parameter discovery
- Add Dockerfile, entrypoint.py, meta.yml from original implementation
- Update paths to use /omic/eureka/Pocketminer/ convention
- Update .gitignore to allow params.json
 2026-03-23 13:27:40 +01:00