Milab 6848 fix sc tcr chain labels

[mchernys]

Greptile Summary

This PR aligns single-cell receptor-chain selection with the pl7.app/vdj/scClonotypeChain producer domain and replaces raw chain letters with biological names in generated labels.

Important touched terms

• ScChain — The persisted "A" | "B" single-cell chain-domain value. Its documented meaning is clarified: A represents Heavy/Beta/Delta, while B represents Light/Alpha/Gamma.
• BlockArgs.scClonotypeChain — The workflow-facing selected domain letter. It replaces the ambiguous scChain argument so the convention is explicit and intentionally invalidates stale executions.
• pl7.app/vdj/scClonotypeChain — The source-column domain used to distinguish paired receptor chains. The workflow now compares the selected letter directly instead of inverting TCR letters.
• chainName — The receptor-specific biological display name derived from a chain letter. Generated V and CDR3 spectratype labels now use names such as Alpha, Beta, Heavy, and Light.
• scChainNames — The workflow mapping from receptor and domain letter to biological chain name.
• TCRAB/TCRGD chain options — UI values are remapped so Alpha/Gamma use B and Beta/Delta use A, while retaining the conventional biological display order.
• Build tooling catalog — @platforma-sdk/block-tools moves from 2.12.6 to 2.14.3 and @platforma-sdk/tengo-builder from 4.0.18 to 4.0.23, with corresponding lockfile updates.

Confidence Score: 5/5

The PR appears safe to merge because the model, UI, and workflow consistently use the corrected chain-domain convention.

The selected domain letter is projected consistently, matched directly against primary source columns, and translated to the corresponding biological name only for display; no blocking failure remains.

Important Files Changed

Filename	Overview
model/src/index.ts	Projects the persisted chain choice under the clearer scClonotypeChain workflow argument name.
model/src/types.ts	Documents the domain-letter semantics and updates the workflow argument contract.
ui/src/utils.ts	Corrects TCRAB and TCRGD option values to match producer-domain letters while preserving biological display order.
workflow/src/main.tpl.tengo	Removes TCR letter inversion, selects source columns directly by domain letter, and emits receptor-specific chain names in result labels.
pnpm-workspace.yaml	Updates the block and Tengo build-tool catalog versions.
pnpm-lock.yaml	Regenerates the transitive dependency graph for the build-tool upgrades.
.changeset/sc-chain-domain-letters.md	Records package releases, changed chain semantics, stale-execution behavior, and user migration guidance.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  U[UI chain option] -->|Alpha/Gamma = B<br/>Beta/Delta = A| D[scClonotypeChain domain letter]
  D --> P[Model argument projection]
  P --> W[Workflow source-column predicate]
  W --> C[Matching primary CDR3 and V-gene columns]
  D --> N[Receptor-specific chain-name mapping]
  N --> L[Biological output labels]
  C --> R[Spectratype results]
  L --> R

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_{Reviews (1): Last reviewed commit: "MILAB-6848: rename the args chain field ..." | Re-trigger Greptile}

Context used (5)

• Context used - Terms is a types in codebase. Provide the list of ... (source)
• Knowledge Base — Spectratype labels and types
• Knowledge Base — Spectratype visualization UI
• Knowledge Base — Spectratype workflow integration
• Knowledge Base — Spectratype quality and release automation