@platforma-open/milaboratories.mixcr-clonotyping-2 2.21.3 → 2.22.0
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- package/block-pack/CHANGELOG.md +49 -0
- package/block-pack/main.plj.gz +0 -0
- package/block-pack/manifest.json +1 -1
- package/block-pack/model.json +1 -1
- package/block-pack/published.json +1 -1
- package/block-pack/ui.tgz +0 -0
- package/dist/AGENTS.d.ts +106 -95
- package/dist/AGENTS.d.ts.map +1 -1
- package/dist/index.d.ts +106 -95
- package/dist/index.d.ts.map +1 -1
- package/dist/index.js +9239 -8132
- package/dist/index.js.map +1 -1
- package/package.json +11 -9
package/block-pack/CHANGELOG.md
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# @platforma-open/milaboratories.mixcr-clonotyping
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## 2.22.0
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### Minor Changes
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- d8c1472: Add the mandatory block kind and migrate the model to the new column access API
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The block now declares a `kind/` package carrying its identity and its
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init-params contract — the fields a project template supplies to seed a new
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instance. The model consumes them in `init` and projects the same set back out
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via `templateParams`, so export and apply are inverses. File-valued params are
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narrowed to `index://` handles, since an `upload://` handle names an import
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local to one machine and would not resolve after a template is applied
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elsewhere.
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Model column access moves off the removed/deprecated surface: `ColumnLazy` →
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`DataColumn`, `resultPool.getSpecByRef` → `Column(ref).getSpec()`, and all three
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`getPColumns()` call sites → `ColumnsCollection`, which resolves ids host-side
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instead of materialising specs and data in the sandbox.
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## 2.21.4
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### Patch Changes
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- 9f35bb7: fix: size the exportClones execs from the .clns instead of a flat 12 GiB
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`exportClones` requested a constant 12 GiB (or `perProcessMemGB / 4`) — a number
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unrelated to what the command holds in memory. It reads the entire CloneSet into
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heap, and single-cell exports then materialise a second, expanded list — one clone
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per (clonotype × cell), each with its own split TagCount — then sort and re-rank it.
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`--chains` filters only after that division, so exporting one chain group still pays
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the whole-file cost.
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Under the `memory-from-limits` entrypoint a 12 GiB grant yields 8788 MiB of heap,
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because the non-heap reserve is a flat 3500 MiB. A 10.7k-cell / 26.7k-clone 10x BCR
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sample exhausted it: `exportClones` died with `OutOfMemoryError`, taking the
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`clonotypes`, `clonotypeTables` and `qcReportTable` outputs with it.
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- RAM is now `clamp(perByte × size(clns), floor, 128 GiB)` — 16 GiB and 16× for the
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bulk export, 24 GiB and 32× for the single-cell export, which pays the per-cell
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expansion. 24 GiB yields 20889 MiB of heap, 2.4× the ceiling that failed. The floors
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are kept tight because `-Xms` is half the grant: the request is a hard pre-allocation,
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and a sample runs one bulk plus one single-cell export per chain group.
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- An Advanced Settings memory override now applies as-is rather than quartered,
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matching how the analyze step treats the same setting. Projects that set it will
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request 4× more for the export step than before.
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- The two PTabler steps now inherit workflow-tengo 6.8's built-in input-volume
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formula, as the rest of the single-cell pipeline already does. They previously took
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⅔ of the mixcr step's budget.
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## 2.21.3
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### Patch Changes
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package/block-pack/main.plj.gz
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Binary file
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package/block-pack/manifest.json
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{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"mixcr-clonotyping-2","version":"2.
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{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"mixcr-clonotyping-2","version":"2.22.0"},"components":{"workflow":{"type":"workflow-v1","main":{"type":"relative","path":"main.plj.gz"}},"model":{"type":"relative","path":"model.json"},"ui":{"type":"relative","path":"ui.tgz"}},"meta":{"title":"MiXCR Clonotyping","description":"Extract TCR / BCR clonotypes from next-generation sequencing data","longDescription":{"type":"relative","path":"description.md"},"changelog":{"type":"relative","path":"CHANGELOG.md"},"logo":{"type":"relative","path":"block-logo.png"},"url":"https://github.com/platforma-open/mixcr-clonotyping-2","support":"mailto:support@milaboratories.com","tags":["upstream","airr","vdj","single-cell"],"organization":{"name":"MiLaboratories Inc","url":"https://milaboratories.com/","logo":{"type":"relative","path":"organization-logo.png"}},"marketplaceRanking":16900},"featureFlags":{"supportsLazyState":true,"supportsPframeQueryRanking":true,"requiresUIAPIVersion":3,"requiresModelAPIVersion":2,"requiresCreatePTable":2,"requiresPFramesVersion":1001031,"requiresPFrameSpec":true,"requiresPFrame":true,"requiresDialog":true,"requiresColumnsCollection":true},"kind":"@platforma-open/milaboratories.mixcr-clonotyping-2.kind@1.1.0"},"timestamp":1787228427163,"files":[{"name":"main.plj.gz","size":1523340,"sha256":"404DFE6E0B8735EE89D000749B749810DAFEBF5AF78B1B60ECEF2C6138BD5C57"},{"name":"model.json","size":575939,"sha256":"ABE8B2BA1F3818F65E7E58D81B8C72FB3274CFEDA89BC2F0F5D9AF8FE0D6C416"},{"name":"ui.tgz","size":4040793,"sha256":"B29BCB98ACAC9DCB451FD9452BAB4528BB3F61B25672B15EE726BB89C02A962D"},{"name":"organization-logo.png","size":24439,"sha256":"FA71390C77C91E4B7FAAE5640D00F92F1E3F2869296F68B6040DD7CC549A50B5"},{"name":"description.md","size":1148,"sha256":"B319CBECC5055A89194C4D7B5768E1ABDE225053885800179439839408ECBA54"},{"name":"CHANGELOG.md","size":44187,"sha256":"C877ED13603E450D8EDAA439558CF7E0D1F6F6D0D5727D100C46B3E0839FAAD5"},{"name":"block-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"}]}
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