Docs · BioCost

BioCost docs for run analysis and reporting

Use this lane when the problem is deterministic cost reporting: ingesting pipeline outputs, scoring runs, and packaging proof-ready summaries.

Cost analysisNextflowDeterministic reportsProof-ready

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Key sections

Prerequisites Install Deterministic demo check Analyze a Nextflow artifact set Expected outputs Validation checklist

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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

BashRunnable example

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

Deterministic demo check

BashRunnable example

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

BashRunnable example

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):

BashRunnable example

.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