kira-secretion

Deterministic, explainable secretion-state QC for single-cell expression data.

Build requirements

• Rust >= 1.95

Install

Install from crates.io:

cargo install kira-secretion

Usage examples

Standalone run (cell mode):

kira-secretion run \
  --input ./data/inf \
  --out ./out/inf \
  --mode cell \
  --run-mode standalone

Standalone run (sample mode):

kira-secretion run \
  --input ./data/inf \
  --out ./out/inf-sample \
  --mode sample \
  --run-mode standalone

Pipeline run (shared cache lookup + pipeline artifacts):

kira-secretion run \
  --input ./data/scc \
  --out ./out/scc-cell \
  --mode cell \
  --run-mode pipeline

Validation command:

kira-secretion validate \
  --input ./data/inf \
  --run-mode pipeline

Panels listing:

kira-secretion panels list

Panels manifest dump:

kira-secretion panels dump --out ./out/panels

Modes

• --run-mode standalone (default): standard MTX/TSV input flow.
• --run-mode pipeline: pipeline contract mode for kira-organelle.

Pipeline cache lookup

In pipeline mode, kira-secretion first searches for shared cache in the input directory:

• exact expected file by prefix:
  • no prefix: kira-organelle.bin
  • prefixed dataset: <PREFIX>.kira-organelle.bin
• if exact file is missing: any file ending with kira-organelle.bin (deterministic lexicographic choice when multiple match)

Behavior:

• cache exists and valid: use shared cache path.
• cache missing: warn once and fall back to MTX input.
• cache exists but invalid: hard error (no silent fallback).

Pipeline output contract

In pipeline mode, outputs are written to:

• --out <DIR> -> <DIR>/kira-secretion/

Required artifacts:

• secretion.tsv (per-cell contract table)
• summary.json (run-level aggregates)
• panels_report.tsv (panel audit)
• pipeline_step.json (ingestion manifest for kira-organelle)

All TSV float values are fixed %.6f.

Shared cache specification

• Cache format specification: kira-shared-sc-cache/CACHE_FILE.md