Docs · OGN platform

GPU-native genomics operating system

From raw reads to GIAB-validated variant calls in a continuous GPU pipeline. This is the control surface for the engine: CLI, pipelines, benchmarks, and deployment runbooks.

CUDA 12+Hopper · AmpereGIAB-validated flowsSchemas stable

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BioCost quickstart

BioCost quickstart Docs overview Benchmark pack Example pipelines GitHub

BioCost quickstart

BioCost is an in silico optimization and verification workflow for Nextflow artifact sets. This page gets you from install to deterministic outputs quickly.

Prerequisites

Python 3.12+
Local BioCost checkout at ~/BioCost (or adjust commands to your path)

Install

BashPowerShellPython API (coming)

ogn CLI

cd ~/BioCost
python3 -m venv .venv
. .venv/bin/activate
python -m pip install -e '.[dev]'

Deterministic demo check

BashPowerShellPython API (coming)

ogn CLI

cd ~/BioCost
. .venv/bin/activate
./demo/run_demo.sh --check

This verifies the deterministic demo path and writes reproducible run artifacts.

Analyze a Nextflow artifact set

BashPowerShellPython API (coming)

ogn CLI

cd ~/BioCost
. .venv/bin/activate
RUN_DIR="$(.venv/bin/costopt ingest /path/to/nextflow/artifacts /tmp/costopt-runs)"
.venv/bin/costopt analyze "$RUN_DIR"
.venv/bin/costopt report "$RUN_DIR"
.venv/bin/costopt patch_nextflow "$RUN_DIR" /path/to/nextflow.config
.venv/bin/costopt verify "$RUN_DIR"
echo "$RUN_DIR"

Optional explicit trace selection (when raw/ has multiple trace candidates):

BashPowerShellPython API (coming)

ogn CLI

.venv/bin/costopt analyze "$RUN_DIR" --trace traces/trace.txt

--trace must be a relative path under raw/.

Expected outputs

After the run, RUN_DIR should contain:

report.html
run_summary.json
recommendations.json
nextflow_config_patch.txt
receipt.json

Validation checklist

costopt verify passes on the generated run directory
run_summary.json and receipt.json exist and are parseable JSON
run_summary.json.trace_path points to the selected trace path under raw/
nextflow_config_patch.txt is generated when a patch is requested