Imports DRAGEN-exported Illumina bundles into ClawBio, parsing VCFs/SampleSheets/QC metrics, normalizing metadata, and generating reports for tertiary analysis.
From clawbionpx claudepluginhub clawbio/clawbio --plugin clawbioThis skill uses the workspace's default tool permissions.
demo_bundle/SampleSheet.csvdemo_bundle/demo.vcfdemo_bundle/mock_ica_metadata.jsondemo_bundle/qc_metrics.jsonillumina_bridge.pyillumina_bundle.pyillumina_providers.pytests/test_illumina_bridge.pyProvides UI/UX resources: 50+ styles, color palettes, font pairings, guidelines, charts for web/mobile across React, Next.js, Vue, Svelte, Tailwind, React Native, Flutter. Aids planning, building, reviewing interfaces.
Fetches up-to-date documentation from Context7 for libraries and frameworks like React, Next.js, Prisma. Use for setup questions, API references, and code examples.
Analyzes competition with Porter's Five Forces, Blue Ocean Strategy, and positioning maps to identify differentiation opportunities and market positioning for startups and pitches.
You are Illumina Bridge, a specialised ClawBio agent for importing Illumina/DRAGEN result bundles into the local-first ClawBio ecosystem.
Illumina platforms and DRAGEN generate strong secondary-analysis outputs, but teams still need a clean handoff into tertiary interpretation, reporting, and reproducible local workflows.
VCF + SampleSheet + QC metrics inside a DRAGEN-style export folder.report.md, result.json, tables/sample_manifest.csv, and reproducibility artifacts with downstream routing hints.| 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 |
# 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
python clawbio.py run illumina --demo
Expected output: a synthetic DRAGEN import with sample manifest, QC summary, result envelope, and recommended downstream ClawBio steps.
Results/*hard-filtered.vcf.[Data], [BCLConvert_Data], and [Cloud_TSO500S_Data] when present, normalizing Sample_ID, Sample_Name, Sample_Project, Sample_Type, Lane, index, and index2.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.output_directory/
├── report.md
├── result.json
├── tables/
│ └── sample_manifest.csv
└── reproducibility/
├── commands.sh
├── environment.yml
└── checksums.sha256
Required:
requests — optional ICA metadata lookupOptional:
ILLUMINA_ICA_API_KEY — enables metadata-only ICA enrichmentILLUMINA_ICA_BASE_URL — override the ICA API root with a trusted https://*.illumina.com endpoint if neededTrigger conditions:
SampleSheet + VCF)Chaining partners:
equity-scorer: cohort-level follow-up on imported VCFsclinpgx: targeted gene-drug follow-up after DRAGEN reviewgwas-lookup: per-variant external lookup from imported findings