@platforma-open/milaboratories.mixcr-clonotyping-2 2.23.1 → 2.23.3
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package/block-pack/CHANGELOG.md
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# @platforma-open/milaboratories.mixcr-clonotyping
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## 2.23.3
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### Patch Changes
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- 2dc34c8: fix: size the QC exportClones steps from the .clns
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The QC report runs `exportClones` twice more per sample — once for the bulk out-of-frame /
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stop-codon counts and once per chain in single-cell mode — and both asked for a flat 16 GiB.
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`exportClones` loads the whole CloneSet and applies `--chains` after the load, so those runs
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cost what the main clonotype export costs; only the column list is smaller. On a large `.clns`
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they OOM at the 12.8 GiB heap the `main` entrypoint hands the JVM out of 16 GiB, while the main
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export beside them now gets a request sized from the file.
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Both now use the same rule as the main export, moved into `:mem-formula` as `exportRam`:
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ram = clamp(8 GiB + perByte x size(clns), floorGiB, 256 GiB)
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with `floorGiB` 24 and `perByte` 30. The report template also moves from the `main` MiXCR
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entrypoint to `memory-from-limits`, which every other template in the block already uses. The
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entrypoint sets the heap fraction the JVM gets, so one entrypoint means one coefficient.
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The `perProcessMemGB` override now raises the floor instead of replacing the rule. A project
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that set it below the floor requested that value and OOMed; a value below the floor now has no
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effect, and the data term still applies above one above it. This is how
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`aggregate-by-clonotype-key` already treats the same override. An override above the 256 GiB
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cap also raises the cap — `between()` asserts `lo <= hi`, so a floor raised past a fixed cap
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would have failed the step outright rather than clamped.
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## 2.23.2
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### Patch Changes
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- 732f0c6: fix: size the exportClones formula from the measured regression
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The bulk export rule was `clamp(16 x size(clns), 16 GiB, 128 GiB)`. Five measured samples,
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with a `.clns` from 0.13 to 1.31 GiB, show that the rule gives the two largest samples 40%
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less memory than they use:
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| `.clns` GiB | measured peak | old grant | new grant |
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| ----------: | ------------: | -----------: | --------: |
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| 0.125 | 10.31 | 16.00 | 16.00 |
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| 0.152 | 10.57 | 16.00 | 16.00 |
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| 0.410 | 15.86 | 16.00 | 20.31 |
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| 1.116 | 30.76 | 17.85 (fail) | 41.48 |
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| 1.308 | 42.26 | 20.92 (fail) | 47.23 |
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The fit is `export peak = 6.4 + 25.0 x clns_GiB`, with R2 0.970. The `memory-from-limits`
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entrypoint gives `-Xmx = 0.85 x grant`. The grant must therefore carry the peak divided by
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0.85, which is `7.5 + 29.4 x clns_GiB`. Three values change:
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- **Intercept, 8 GiB.** JVM overhead and reference-library overhead do not scale with the
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file. The previous rule had no constant term, so it started at zero, and the 16 GiB floor
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did all the work until the file became large enough to fail. The intercept is a fitted
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term and not a second floor, so the formula adds it and does not clamp it.
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It applies to both exports.
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- **Bulk coefficient, 16 to 30.** The single-cell coefficient stays at 32. Every measured
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sample is a bulk export, so no measurement supports or contradicts that value. The
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single-cell path does gain the same intercept, because JVM overhead and reference-library
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overhead do not depend on the path.
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- **Cap, 128 to 256 GiB.** With the new coefficient the old cap applies at a 4.1 GiB
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`.clns`, which a 60M-read sample can reach. It now applies at 8.5 GiB.
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The floors do not change. They are 16 GiB for bulk and 24 GiB for single-cell, and they
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still carry the two smallest samples.
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The template `hash_override` UUID also changes. This forces a one-time recompute of cached
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export results. Without the new UUID the new sizing does not reach a project that has
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already run the export.
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## 2.23.1
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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":"2.23.
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{"schema":"v2","description":{"id":{"organization":"milaboratories","name":"mixcr-clonotyping-2","version":"2.23.3"},"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":1789671515912,"files":[{"name":"main.plj.gz","size":1560792,"sha256":"C316C0D7E55C04315CDB9BA50A8B3F7DD96139D044E28027A3C00CC939287AC2"},{"name":"model.json","size":575939,"sha256":"ABE8B2BA1F3818F65E7E58D81B8C72FB3274CFEDA89BC2F0F5D9AF8FE0D6C416"},{"name":"ui.tgz","size":4040755,"sha256":"702CC988A01787A0DE526A9F3D7294615F33626E1CFF61B289E12AC76CC25F5A"},{"name":"organization-logo.png","size":24439,"sha256":"FA71390C77C91E4B7FAAE5640D00F92F1E3F2869296F68B6040DD7CC549A50B5"},{"name":"description.md","size":1148,"sha256":"B319CBECC5055A89194C4D7B5768E1ABDE225053885800179439839408ECBA54"},{"name":"CHANGELOG.md","size":48766,"sha256":"C1B262960BECE0A22A780D04BA474A25837E9F6B8C8571901952FD374846320B"},{"name":"block-logo.png","size":21527,"sha256":"6BB33BAF0CD039549661B51AE490373BE60D1811EC71F5023400928293BC2427"}]}
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package/block-pack/ui.tgz
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package/package.json
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{
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"name": "@platforma-open/milaboratories.mixcr-clonotyping-2",
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"version": "2.23.
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"version": "2.23.3",
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"files": [
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"dist",
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"block-pack"
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"devDependencies": {
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"@milaboratories/ts-builder": "1.7.0",
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"@milaboratories/ts-configs": "1.4.0",
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"@platforma-sdk/block-tools": "2.
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"@platforma-sdk/block-tools": "2.16.0",
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"@platforma-sdk/model": "1.82.0",
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"shx": "^0.4.0",
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"typescript": "~5.6.3",
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"@platforma-open/milaboratories.mixcr-clonotyping-2.kind": "1.1.0",
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"@platforma-open/milaboratories.mixcr-clonotyping-2.workflow": "3.29.
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"@platforma-open/milaboratories.mixcr-clonotyping-2.
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"@platforma-open/milaboratories.mixcr-clonotyping-2.
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"@platforma-open/milaboratories.mixcr-clonotyping-2.workflow": "3.29.3",
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"@platforma-open/milaboratories.mixcr-clonotyping-2.model": "1.28.0",
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"@platforma-open/milaboratories.mixcr-clonotyping-2.ui": "1.27.3"
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},
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"block": {
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"components": {
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