Ready to supercharge your AI agents?

Install any skill in seconds. Free to start, no credit card required.

Get Started Free →

Illumina Bridge · clawbio | DecimalAI

scienceby clawbio

Illumina Bridge

clawbio/illumina-bridge

Source clawbio/clawbio ↗License MIT

Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.

SkillScore91Maintained

Automatic

Data Engineer pack

Last verified 8/16/2026

What it changes

Passed 20 of 22 test cases with the skill, and 5 of 22 without it.

Without skill23%

With skill91%

Checks it passed that the model alone missed

The output specification includes report.md.
The output specification includes result.json.
The output includes reproducibility/commands.sh.

and 22 more in the full report

15 fixed5 passed either way2 still failing0 broke

Pass-rate lift: +68 pp
Tokens: +21%
Agent turns: 0%
Response time: -55%

Model gemini-3.6-flashMeasured 8/16/2026v120 of 22 cases passed with skill

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/clawbio-illumina-bridge/SKILL.md https://app.decimal.ai/s/clawbio-illumina-bridge/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add clawbio-illumina-bridge, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/clawbio-illumina-bridge/ and pins it in .decimal/skills.lock

decimalai skills add clawbio-illumina-bridge

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/clawbio-illumina-bridge/SKILL.md https://app.decimal.ai/s/clawbio-illumina-bridge/SKILL.md

Raw file: /s/clawbio-illumina-bridge/SKILL.md ↗ · machine-readable summary at /s/clawbio-illumina-bridge.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 15 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 15

Prompt

What filename is used for the structured JSON envelope written at the root of the import output directory?

What was checked, without and with the skill
Checked	Without skill	With skill
The structured JSON output is written to result.json.	Missed	Passed

case-22 · gemini-3.6-flash · 8/16/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md125 linessingle file

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

Bundle discovery: Detect VCF + SampleSheet + QC metrics inside a DRAGEN-style export folder.
Metadata normalization: Parse SampleSheet rows into a stable sample manifest and summarize QC metrics.
Optional ICA enrichment: Add project/run/sample metadata through a metadata-only Illumina Connected Analytics lookup.
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

Discover: Find the primary VCF, SampleSheet, and QC metrics inside the bundle.
Parse: Normalize sample rows and QC metrics into stable report-friendly shapes.
Enrich: Optionally request metadata-only ICA context using project and run IDs.
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>

Track record

Benchmark

20 / 22

test cases passed, vs 5 / 22 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

clawbio / clawbio

skills/illumina-bridge/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

Illumina Bridge

Why This Exists

Core Capabilities

Input Formats

Workflow

CLI Reference

Track record

Benchmark

Adoption

SkillSafety

Source

Related skills