Illumina bridge

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 metadata, 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 project/run/sample metadata through a metadata-only Illumina Connected Analytics lookup.
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 context using project and run IDs.
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 <run_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.

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, request project and analysis metadata using the API key from the environment and merge sample-level metadata when available.
5. Output contract: Emit report, manifest, and reproducibility artifacts without launching downstream skills automatically.

Example Queries

• "Import this DRAGEN export from Illumina and tell me what I can do next"
• "Read this SampleSheet and VCF bundle from DRAGEN"
• "Add ICA project metadata to this Illumina bundle"

Output Structure

output_directory/
├── report.md
├── result.json
├── tables/
│   └── sample_manifest.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256

Dependencies

Required:

• requests — optional ICA metadata lookup

Optional:

• ILLUMINA_ICA_API_KEY — enables metadata-only ICA enrichment
• ILLUMINA_ICA_BASE_URL — override the ICA API root with a trusted https://*.illumina.com endpoint if needed

Safety

• Local-first: genomic files are read locally; the skill never uploads VCF payloads
• Metadata-only cloud access: ICA enrichment is opt-in and limited to project/run metadata
• Disclaimer: every report includes the ClawBio medical disclaimer
• Reproducibility: commands, environment context, and checksums are always written

Integration with Bio Orchestrator

Trigger conditions:

• queries mentioning Illumina, DRAGEN, ICA, BaseSpace, SampleSheet, or sample sheet
• directories that contain a recognizable Illumina bundle (SampleSheet + VCF)

Chaining partners:

• equity-scorer: cohort-level follow-up on imported VCFs
• clinpgx: targeted gene-drug follow-up after DRAGEN review
• gwas-lookup: per-variant external lookup from imported findings

Citations

• DRAGEN secondary analysis
• Illumina Connected Analytics
• BCL Convert Sample Sheet