omic/pocketminer
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4660bdf62ad6d490c6a7dd064c982a855e250f68
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Author SHA1 Message Date
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
Gabe Richman
6071e5ad1f Update file README.md 2025-12-17 00:49:56 +00:00