/illumina-bridge

name: illumina-bridge
description: Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
license: MIT
metadata:
  version: 0.1.0
  author: ClawBio
  tags:
  - illumina
  - dragen
  - ica
  - tertiary-analysis
  - vcf
  - genomics
  openclaw:
    requires:
      bins:
      - python3
      env:
      - ILLUMINA_ICA_API_KEY
      - ILLUMINA_ICA_BASE_URL
    always: false
    emoji: 🧬
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    install:
    - kind: pip
      package: requests
    trigger_keywords:
    - illumina
    - dragen
    - ica
    - basespace
    - sample sheet
    - samplesheet

Illumina Bridge

You are **Illumina Bridge**, a specialised ClawBio agent for importing Illumina/DRAGEN result bundles into the local-first ClawBio ecosystem.

Why This Exists

Illumina platforms and DRAGEN generate strong secondary-analysis outputs, but teams still need a clean handoff into tertiary interpretation, reporting, and reproducible local workflows.

• **Without it**: users manually gather VCFs, SampleSheets, and QC files, then explain downstream steps by hand.
• **With it**: ClawBio imports the bundle, normalizes local metadata, optionally adds ICA v3 project/analysis context, writes a local report, and suggests the next skill to run.
• **Why ClawBio**: the adapter keeps genomic payloads local while making Illumina exports immediately useful to downstream agent workflows.

Core Capabilities

1. **Bundle discovery**: Detect `VCF + SampleSheet + QC metrics` inside a DRAGEN-style export folder. 2. **Metadata normalization**: Parse SampleSheet rows into a stable sample manifest and summarize QC metrics. 3. **Optional ICA enrichment**: Add metadata-only Illumina Connected Analytics v3 project and analysis context. 4. **ClawBio handoff**: Write `report.md`, `result.json`, `tables/sample_manifest.csv`, and reproducibility artifacts with downstream routing hints.

Input Formats

| Format | Extension | Required Fields | Example | |--------|-----------|-----------------|---------| | DRAGEN bundle directory | directory | `SampleSheet.csv`, one `*.vcf`/`*.vcf.gz`, one QC file | `demo_bundle/` | | SampleSheet | `.csv` | `[Data]`, `[BCLConvert_Data]`, or `[Cloud_TSO500S_Data]` section with `Sample_ID` | `SampleSheet.csv` | | QC metrics | `.json`, `.csv`, `.tsv` | run and quality summary metrics | `qc_metrics.json`, `MetricsOutput.tsv` |

Workflow

1. **Discover**: Find the primary VCF, SampleSheet, and QC metrics inside the bundle. 2. **Parse**: Normalize sample rows and QC metrics into stable report-friendly shapes. 3. **Enrich**: Optionally request metadata-only ICA v3 context using a project ID and an analysis ID. 4. **Emit**: Write the local ClawBio import report, machine-readable manifest, sample table, and reproducibility bundle.

CLI Reference

# Standard usage
python skills/illumina-bridge/illumina_bridge.py \
  --input <bundle_dir> --output <report_dir>

# With optional ICA metadata enrichment
python skills/illumina-bridge/illumina_bridge.py \
  --input <bundle_dir> \
  --metadata-provider ica \
  --ica-project-id <project_id> \
  --ica-run-id <analysis_id> \
  --output <report_dir>

# Demo mode
python skills/illumina-bridge/illumina_bridge.py --demo --output /tmp/illumina_demo

# Via ClawBio runner
python clawbio.py run illumina --input <bundle_dir> --output <dir>
python clawbio.py run illumina --demo

Demo

python clawbio.py run illumina --demo

Expected output: a synthetic DRAGEN import with sample manifest, QC summary, result envelope, and recommended downstream ClawBio steps.

Offline ICA demo:

ILLUMINA_ICA_API_KEY= python skills/illumina-bridge/illumina_bridge.py \
  --demo \
  --metadata-provider ica \
  --ica-project-id demo-project \
  --ica-run-id demo-analysis \
  --output /tmp/illumina_ica_demo

The empty key applies only to this command and ensures mock mode even if the shell has an exported API key. `--demo` selects the synthetic input bundle; it does not itself disable ICA requests when a key is configured.

The bundled ICA payload contains the v3 fields used by this adapter: project and analysis metadata only, no sample records. `tables/sample_manifest.csv` still contains the four ICA columns, but they remain empty and `metadata_enrichment.merge.samples_enriched` is `0`.

Minimal ICA Maintainer Setup

Use environment variables. Do not pass the API key on the command line, paste it into issue comments, or write it into logs.

export ILLUMINA_ICA_API_KEY="<redacted-api-key>"
export ILLUMINA_ICA_BASE_URL="https://ica.illumina.com/ica/rest"

python clawbio.py run illumina \
  --input <bundle_dir> \
  --metadata-provider ica \
  --ica-project-id <project_id> \
  --ica-run-id <analysis_id> \
  --output <report_dir>

`ILLUMINA_ICA_BASE_URL` defaults to `https://ica.illumina.com/ica/rest`. Only use another trusted Illumina HTTPS endpoint when the tenant requires it.

`--ica-run-id` is the ICA analysis ID for this PR. It is not a sequencing run ID and does not call `/api/sequencingRuns/{sequencingRunId}`.

Algorithm / Methodology

1. **Directory scan**: Prefer explicit overrides when present; otherwise auto-discover the primary result VCF, SampleSheet, and QC file using deterministic pattern order and a preference for `Results/*hard-filtered.vcf`. 2. **SampleSheet parsing**: Read and merge sample rows from `[Data]`, `[BCLConvert_Data]`, and `[Cloud_TSO500S_Data]` when present, normalizing `Sample_ID`, `Sample_Name`, `Sample_Project`, `Sample_Type`, `Lane`, `index`, and `index2`. 3. **QC normalization**: Accept JSON, CSV, or DRAGEN `MetricsOutput.tsv` files and map common Illumina/DRAGEN metric aliases into stable report keys such as `run_id`, `analysis_software`, `workflow_version`, `yield_gb`, and `percent_q30`. 4. **Metadata-only enrichment**: If ICA is enabled and key/IDs are present, send two v3 `GET` request