Question: Can a resource-aware SNAP + Sprocket orchestrator replace manual LSF wiring for scalable single-cell analysis?
Expected output: Tested downstream launcher (for two Snap modules), documented HPC test results, code-review notes, 3-slide deck, 2-minute lightning talk, and live demo for judges.
Team lead: Antonia Chroni (@AntoniaChroni)
Code review & development leads: Clay McLeod, Emma Bishop, Antonia Chroni
Dry-run & HPC testers: Clay McLeod, Antonia Chroni, Rojina Sapkota (only St Jude HPC users)
Biology assessment leads: Rachana Pandey, A.S.M. Tanjim Hassan
WDL and ROI analysis leads: Lindsey Warren, Sarthak Sunil Dhanke
Slack: Team channel (team15)
| Doc | Purpose |
|---|---|
| Hackathon runbook | Team, schedule, test spec (T1–T17), deliverables, checklists, demo prep |
| Problem & solution overview | Slide-ready problem/solution narrative |
| Daedalus pitch | Tool name, 30/60s pitches, naming rationale |
| Participant FAQ | Onboarding: WDL vs bash, resource scaling, pair roles |
| Test log | Live pass/fail log — fill in during the event |
| HPC setup | St. Jude HPC access and modules |
| Team roster (xlsx) | Source of truth for pair assignments |
Quick start: cd analyses/sc-rna-seq-snap-Victoria-Knockout then bash scripts/test-downstream-layout.sh
KIDS26-Team15/
├── analyses/
│ ├── sc-rna-seq-snap-legacy-Victoria-Knockout-shareable Results from Legacy Run
│ └── sc-rna-seq-snap-sprocket-Victoria-Knockout-shareable Results from Daedalus Run
├── data/ project_metadata
└── deliverables/
│ ├── biological-validation-benchmarking/ Biological comparisons and assessments
│ ├── docs/ Pitches, problem overview, participant FAQ
│ ├── reports/ Event report-outs
│ ├── roi-analysis/ ROI analysis
│ ├── slides/ Kickoff deck + event deck (TBD; see README there)
│ └── wdl-stakeholder-evaluation/ Assessment of WDL vs various workflow languages
├── docs/ HPC setup, troubleshooting, learning resources
├── LICENSE.md
├── project-management/
│ ├── hackathon-runbook.md Operational guide (read this before Day 1)
│ └── stjude-biohackathon-kids26-team15-info.xlsx
└── README.md This file
Tools: SNAP (sc-rna-seq-snap), WDL, Sprocket, R/Seurat, Apptainer, LSF, YAML config · Victoria Knockout cohort (4 samples, ~27k cells)
Schedule: Day 1 (4 h) · Day 2 (8 h) · Day 3 (4 h afternoon) · Demo 3:00–6:00 PM
- Branch → focused change → PR → teammate review → merge.
- Do not commit secrets, credentials, or private data.
- See Git and GitHub basics if needed.
Maintainer: KIDS26 Team 15 · Generated during KIDS26 Team 15 Biohackathon 26 (September 16-18, 2026)