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name: domain-routing description: "Choose a ClawBio skill or short skill chain from catalog metadata, file shape, headers, and biological intent." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

ClawBio domain routing

Use this sub-skill when a request names no exact ClawBio capability, supplies a data file, asks which skill to use, or may require a multi-step analysis. This is a routing contract, not a substitute for a specialist skill's scientific method.

Load the right detail

• Read catalog-and-routing.md for catalog semantics, routing order, aliases, and data-shape decisions.
• Read domain-families.md for the family map and common chains.
• Read troubleshooting.md before reporting a missing, ambiguous, stale, or unsafe route.
• For execution and flag policy, hand off to core-runner.
• For Nextflow and other multi-stage wrappers, hand off to pipelines-integrations.
• For a quick metadata lookup, run the bundled read-only catalog query script with an explicit catalog path.

Operating procedure

1. Normalize the request. Record the biological goal, input paths, expected output, reference/build if stated, and whether the user requests one analysis or a chain. Do not infer a clinical diagnosis or silently add a downstream step.
2. Inspect before routing. Confirm that each path exists and inspect a small header or metadata sample locally. Extension alone is not enough: distinguish raw counts from finished DE tables, a VCF from a DTC genotype text file, raw scRNA counts from a processed .h5ad, and a bulk FASTQ from a single-cell FASTQ bundle. Do not upload genomic payloads.
3. Search the catalog. Match trigger_keywords, tags, description, input shape, and chaining_partners; use maturity_evidence.cli_registered to determine whether a cli_alias is actually runnable through clawbio.py run. The catalog is discovery metadata, not proof that every entry is executable.
4. Prefer the narrowest route. A strong explicit biological intent beats a generic extension route. If the user asks for a named registered alias, preserve it unless the input contract contradicts it. If two routes remain plausible, ask one focused clarification and show the competing interpretations.
5. Choose an invocation form. For a registered skill, use its CLI alias, not necessarily its directory name. For an agent-readable-only entry, use its SKILL.md as operating guidance or explain that it is not exposed through clawbio run; never invent an alias. Apply the runner's allow-listed flags; do not bypass allowed_extra_flags.
6. Plan, then execute. For chains, state each handoff and the expected artifact (for example, counts TSV or integrated.h5ad) before running. The runner and pipeline integration skills own command construction, dependency checks, overwrite checks, and reproducibility details.
7. Report uncertainty. If the catalog is missing or stale, distinguish a routing suggestion from a verified executable route. If headers are malformed, the path is missing, or a required backend is unavailable, stop at the appropriate preflight and give a concrete fix.

Fast routing rules

• VCF/VCF.GZ + annotation/ClinVar/VEP/gnomAD: prefer the agent-readable variant annotation guidance; VCF/VCF.GZ + population diversity: registered equity; an rsID association/PheWAS/eQTL question: registered gwas; VCF + PRS: registered just-prs or prs according to the requested model/input contract.
• 23andMe/AncestryDNA raw text + drug, CYP, CPIC, or pharmacogenomics: registered pharmgx; a unified personal report may continue to registered profile.
• FASTQ/BAM/CRAM + QC or alignment: seq-wrangler is agent-readable-only in the inspected catalog; use a registered rnaseq-pipeline, scrnaseq-pipeline, or sarek-pipeline only when the request matches that upstream pipeline and samplesheet contract.
• FASTA + generic sequence/protein metrics: registered analyze-fasta; FASTA plus promoter, splice, enhancer, chromatin, expression, or gene-annotation intent: the corresponding gi-* agent-readable skill. PDB/CIF or structure comparison: struct-predictor guidance.
• .h5ad or 10x Matrix Market: registered scrna for QC, clustering, markers, annotation, and contrasts; scrna-embedding first for scVI/scANVI/latent/integration/batch correction, then hand its latent artifact to scrna when downstream markers or clustering are requested.
• CSV/TSV: inspect headers. Count matrix plus sample metadata and a DE request routes to registered rnaseq; finished DE/marker columns route to registered diffviz; ancestry/population columns plus diversity intent route to equity. Never treat every tabular file as counts.
• Image/PDF figure + digitization or extraction: registered data-extract; proteomics platform tables route by platform (affprot for Olink/SomaScan; proteomics-specific agent-readable guidance for MaxQuant/DIA-NN or clocks).

Safety checkpoint

Before selecting a route, inspect VCF header/version and sample columns, FASTA headers, FASTQ read structure, BAM/CRAM metadata, Matrix Market companion files, .h5ad obs/var/layers/obsm keys, and CSV/TSV column names. Preserve genome build and whether data are raw, processed, or synthetic. Treat a malformed or contradictory header as needs_input, not as permission to guess.

Output of this sub-skill

Return a compact routing record: normalized intent, inspected shape/header signals, candidate names and aliases, registered/agent-readable status, selected route or clarification question, planned chain and artifact handoffs, maturity caveats, and any safety or stale-catalog warning. Then hand off execution to the relevant operating skill; do not run specialist analyses from this router.