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a6a5d8e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 | # @szl-holdings/sequence-pipeline
Multi-stage ingest pipeline with per-stage hashed artefacts and
CI-bearing tabulated statistics. Re-expressed from CRISPResso2's
**pipeline-as-evidence-ledger** shape: every stage emits a
`(inputsHash, paramsHash, outputsHash)` triple so any downstream claim
walks back to the exact data that produced it.
## Doctrine rules enforced
- **No claim without an interval.** `pipeline.tabulated-statistic.v1`
rows with missing CI bounds are rejected at the write boundary.
- **Absence is a row.** When the schema declares the domain has a
meaningful "no event" label, the table must include at least one
`isNegativeSpace: true` row.
## Worked example — edit-call
```ts
import { StagedPipeline, wilsonInterval } from '@szl-holdings/sequence-pipeline';
import { createHash } from 'node:crypto';
const hash = (v: unknown) => createHash('sha256').update(JSON.stringify(v)).digest('hex');
const pipeline = new StagedPipeline({ pipelineId: 'run-001', tooling: { tool: 'edit-call@1.2' }, hash });
const result = await pipeline.run(
rawReads,
[
{ name: 'filter', params: { minQ: 30 }, run: filterReads },
{ name: 'align', params: { ref: 'GRCh38' }, run: alignReads },
{ name: 'classify', params: { caller: 'edit-v1' }, run: callEdits },
],
(final) => buildTabulatedStatistic(final, wilsonInterval),
);
// `result.stages[]` → write each as a `pipeline.stage.v1` receipt.
// `result.tabulatedStatistic` → write as `pipeline.tabulated-statistic.v1`.
```
## Source provenance
Pipeline shape re-expressed (not copied) from
`github.com/standardgalactic/CRISPResso2` (AGPL — upstream).
## Consumers
| Artifact | Use |
|----------|-----------------------------------------------------------|
| Amaru | Sync-envelope ingest as a staged pipeline |
| Sentra | Incident timeline as a staged pipeline (det → triage → ...) |
| api-server | Pipeline receipt-write endpoints (downstream task) |
See [`docs/research/perception-bio-synthesis-2026.md`](../../docs/research/perception-bio-synthesis-2026.md) §2.
|