# @platforma-open/milaboratories.miltenyi-tcr-clonotyping.workflow

## 1.3.3

### Patch Changes

- 74048fa: Switch to miltenyi-human-rna-tcr-profiling preset and update MiXCR to 4.7.0-364-develop

## 1.3.2

### Patch Changes

- 437ec46: Fix sample labels, resolve CID conflicts, set label visibility

## 1.3.1

### Patch Changes

- df1807f: Resolve issues identified in the 2026-05-01 review:

  - Fix `linkerTrace` shadow bug in `process.tpl.tengo` that silently dropped the `pl7.app/trace` annotation on `clns` for every multiplexed run.
  - Replace silent fallback to a domain-less `pl7.app/sampleId` axis with an assert when upstream `traceSource` axes are malformed.
  - Extract Miltenyi kit barcode dictionary into `barcode-dictionary.lib.tengo` — single source of truth shared by `prerun.tpl.tengo` and `fastq-demultiplexing.tpl.tengo`.
  - Extract preset-specific overrides (`tagPattern`, `assemblingFeature`) into `preset-info.lib.tengo` to remove duplicated hardcoded branches and add an assert for unknown presets.
  - Move legacy `preset: string` → `{ type: 'name', name }` shape migration from a UI mount-time side-effect into a `DataModelBuilder.migrate('v2', ...)` step. Removes duplicate work on every UI mount.
  - Drop unconditional init writes from `SettingsPanel.vue` script setup; defaults now flow exclusively from `DataModelBuilder.init()` and the v2 migration. Setting state only changes through user gestures.
  - Mark the prerun-validation-gate watcher as a tolerated hairpin (alongside the block-label exception); drop a reflection for the harness team.

## 1.3.0

### Minor Changes

- e076a97: Restore Miltenyi clonotyping for multiplexed FASTQ inputs after the Samples & Data column refactor (MILAB-6178). The block reads the new `pl7.app/sequencing/multiplexingRules` column when present and falls back to the legacy `sampleGroups` linker. Detection is automatic — open an existing project and Run.

  Accept multi-tag rules columns: the first tag is the demux barcode; remaining tags (chain, donor, antigen, replicate, etc.) are treated as descriptive metadata. Multi-alternative cells remain rejected.

  Existing projects upgrading from a prior version may show a one-time `CIDConflictError` on the first run after the upgrade. Click Run again — the second pass succeeds. Subsequent runs reuse cached results normally.

## 1.2.2

### Patch Changes

- 388e7ea: CID conflict fix

## 1.2.1

### Patch Changes

- 26148ee: Fix wrong file names when exporting data with demultiplexing — exported files were named "undefined\_<chain>.tsv" because sampleLabels mapped group IDs instead of demultiplexed sample IDs

## 1.2.0

### Minor Changes

- 0f2c165: Support custom block title and running status

## 1.1.1

### Patch Changes

- eab850f: Updated naming

## 1.1.0

### Minor Changes

- 63f1378: Initial release
