@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.0.0

package/.turbo/turbo-build.log

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+
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.0.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> rm -rf dist && pl-tengo check && pl-tengo build
+
+Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
+Processing "src/calculate-export-specs.lib.tengo"...
+Processing "src/calculate-preset-info.tpl.tengo"...
+Processing "src/list-presets.tpl.tengo"...
+Processing "src/main.tpl.tengo"...
+Processing "src/mixcr-analyze.tpl.tengo"...
+Processing "src/mixcr-export.tpl.tengo"...
+Processing "src/prerun.tpl.tengo"...
+Processing "src/process.tpl.tengo"...
+Processing "src/test/columns-calculate.tpl.tengo"...
+Processing "src/test/columns.test.tpl.tengo"...
+No syntax errors found.
+  info: Compiling 'dist'...
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/calculate-preset-info.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/list-presets.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/mixcr-analyze.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/mixcr-export.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/prerun.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/process.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/test.columns-calculate.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/test.columns.test.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow/dist/tengo/tpl/main.plj.gz
+  info: 
+  info: Template Pack build done.

package/.turbo/turbo-test.log

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+
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.0.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> vitest
+
+
+ RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+
+ ✓ src/test/columns.test.ts (6 tests) 48242ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 11740ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 7636ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7348ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7318ms
+   ✓ checking preset for 'rna-seq' 7099ms
+   ✓ checking preset for 'generic-single-cell-gex' 7100ms
+
+ Test Files  1 passed (1)
+      Tests  6 passed (6)
+   Start at  16:45:52
+   Duration  48.98s (transform 48ms, setup 0ms, collect 509ms, tests 48.24s, environment 0ms, prepare 63ms)
+

package/CHANGELOG.md

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+# @platforma-open/milaboratories.mixcr-clonotyping.workflow
+
+## 2.0.0
+
+### Major Changes
+
+- f3e6573: First build of MiXCR Clonotyping 2
+  - clonotypeKey based output
+
+## 1.15.0
+
+### Minor Changes
+
+- 5ca4eb7: Check if custom library json file gzipped or not
+- a4dc2aa: Columns annotation for descrete filtering
+
+## 1.14.1
+
+### Patch Changes
+
+- b049d9d: SDK upgrade to fix sporadic validation errors in workflow execution
+
+## 1.14.0
+
+### Minor Changes
+
+- c6b6860: library added to processColumns in precess tpl
+
+## 1.13.0
+
+### Minor Changes
+
+- 95a3ac2: Migration to AggregateV2 API
+
+## 1.12.0
+
+### Minor Changes
+
+- db3cc0a: Custom reference library from library builder block or file
+
+## 1.11.0
+
+### Minor Changes
+
+- 53900ff: productive feature bug correction
+
+## 1.10.0
+
+### Minor Changes
+
+- 8652c07: new columns added
+
+## 1.9.8
+
+### Patch Changes
+
+- 9454329: Update ui-vue to 1.21.21, model to 1.21.20
+
+## 1.9.7
+
+### Patch Changes
+
+- e1fe8bf: revert exec braces
+
+## 1.9.6
+
+### Patch Changes
+
+- a6f9198: wf: escape braces or else backend will try to eval these expressions and fail with error
+
+## 1.9.5
+
+### Patch Changes
+
+- 02b681a: use PlChartStackedBar component
+
+## 1.9.4
+
+### Patch Changes
+
+- 2fbd0c8: Update workflow-sdk to new version (better deduplication and recovery)
+
+## 1.9.3
+
+### Patch Changes
+
+- b2bf6b4: Fix for presets undefined assemlingFeature (i.e. rna-seq)
+
+## 1.9.2
+
+### Patch Changes
+
+- 87757bd: SDK upgrade
+
+## 1.9.1
+
+### Patch Changes
+
+- 54155d9: SDK upgrade
+- 54155d9: Export clns column label correction
+
+## 1.9.0
+
+### Minor Changes
+
+- 9ccb1fd: Support of trace annotations; SDK upgrade
+
+## 1.8.2
+
+### Patch Changes
+
+- 1f25d8e: Output colums ordering. SDK upgrade, preset list fixes.
+
+## 1.8.1
+
+### Patch Changes
+
+- af5b969: Fix for blinking dropdowns, align reports are now loaded as soon as possible, migration to new SDK.
+
+## 1.8.0
+
+### Minor Changes
+
+- e6fb4f5: Fasta input support. Major SDK upgrade.
+
+## 1.7.0
+
+### Minor Changes
+
+- fddc283: - Cache MiXCR results for 48h
+  - Migrate to new pfconv params & fix columns
+
+## 1.6.2
+
+### Patch Changes
+
+- 204e8ff: Fix alphabet annotation
+
+## 1.6.1
+
+### Patch Changes
+
+- 87eb0db: WF SDK Upgrade, PFrames export fix
+- dc4c8c7: SDK upgrade
+
+## 1.6.0
+
+### Minor Changes
+
+- 6ac0c86: "pl7.app/table/visibility" & "pl7.app/table/orderPriority" annotations added to export columns
+- abd805e: Fix for export table columns for single-cell results
+
+### Patch Changes
+
+- 6ac0c86: Fix for dense annotation
+
+## 1.5.1
+
+### Patch Changes
+
+- 6c574ab: SDK upgrade
+
+## 1.5.0
+
+### Minor Changes
+
+- ba1094c: Multilate fastq support.
+
+## 1.4.1
+
+### Patch Changes
+
+- 4e79c1d: Preset file support & SDK upgrade
+
+## 1.4.0
+
+### Minor Changes
+
+- 5238326: Now block exports \*.assembledCells.clns for presets where cell assembly is applied to the data
+
+### Patch Changes
+
+- 5238326: SDK upgrade
+
+## 1.3.0
+
+### Minor Changes
+
+- 50f6bae: mixcr software upgrade, new version should allocate 85% of available memory in container environment
+
+### Patch Changes
+
+- 11af733: workflow: bump wf, fix paths on windows in workdir lib
+- 797f5bf: all preset-export / -list mixcr commands moved to ui execution queue to prevent blocking of initial execution setup and subsequent online deduplication
+
+## 1.2.1
+
+### Patch Changes
+
+- 9a99a0d: SDK upgrade
+- 9a99a0d: fixes error when using presets with floating assembling features
+
+## 1.2.0
+
+### Minor Changes
+
+- ffe5dc0: - Update Platforma SDK
+  - Fix block deduplication bug
+  - Better styles for the table component
+  - Fix annotation of export counts
+  - Fix chain axis nature (scaleCompatible)
+
+## 1.1.4
+
+### Patch Changes
+
+- 4b70a39: chore: fix software.mixcr pkg name
+
+## 1.1.3
+
+### Patch Changes
+
+- be26771: Pass MI_LICENSE secret to mixcr commands
+
+## 1.1.2
+
+### Patch Changes
+
+- Logo update
+
+## 1.1.1
+
+### Patch Changes
+
+- 99b1a7f: SDK upgrade & secrets API usage in workflow
+
+## 1.1.0
+
+### Minor Changes
+
+- db5308b: migration to pl-open
+
+## 1.0.1
+
+### Patch Changes
+
+- 3a4df33: Initial release

package/dist/index.d.ts

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+declare type TemplateFromFile = { readonly type: "from-file"; readonly path: string; };
+declare type TplName = "aggregate-by-clonotype-key" | "calculate-preset-info" | "list-presets" | "mixcr-analyze" | "mixcr-export" | "prerun" | "process" | "test.columns-calculate" | "test.columns.test" | "main";
+declare const Templates: Record<TplName, TemplateFromFile>;
+export { Templates };

package/dist/index.js

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+module.exports = { Templates: {
+  'aggregate-by-clonotype-key': { type: 'from-file', path: require.resolve('./tengo/tpl/aggregate-by-clonotype-key.plj.gz') },
+  'calculate-preset-info': { type: 'from-file', path: require.resolve('./tengo/tpl/calculate-preset-info.plj.gz') },
+  'list-presets': { type: 'from-file', path: require.resolve('./tengo/tpl/list-presets.plj.gz') },
+  'mixcr-analyze': { type: 'from-file', path: require.resolve('./tengo/tpl/mixcr-analyze.plj.gz') },
+  'mixcr-export': { type: 'from-file', path: require.resolve('./tengo/tpl/mixcr-export.plj.gz') },
+  'prerun': { type: 'from-file', path: require.resolve('./tengo/tpl/prerun.plj.gz') },
+  'process': { type: 'from-file', path: require.resolve('./tengo/tpl/process.plj.gz') },
+  'test.columns-calculate': { type: 'from-file', path: require.resolve('./tengo/tpl/test.columns-calculate.plj.gz') },
+  'test.columns.test': { type: 'from-file', path: require.resolve('./tengo/tpl/test.columns.test.plj.gz') },
+  'main': { type: 'from-file', path: require.resolve('./tengo/tpl/main.plj.gz') }
+}};

package/dist/index.mjs

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+import { resolve } from 'node:path';
+export const Templates = {
+  'aggregate-by-clonotype-key': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/aggregate-by-clonotype-key.plj.gz') },
+  'calculate-preset-info': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/calculate-preset-info.plj.gz') },
+  'list-presets': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/list-presets.plj.gz') },
+  'mixcr-analyze': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/mixcr-analyze.plj.gz') },
+  'mixcr-export': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/mixcr-export.plj.gz') },
+  'prerun': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/prerun.plj.gz') },
+  'process': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/process.plj.gz') },
+  'test.columns-calculate': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/test.columns-calculate.plj.gz') },
+  'test.columns.test': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/test.columns.test.plj.gz') },
+  'main': { type: 'from-file', path: resolve(import.meta.dirname, './tengo/tpl/main.plj.gz') }
+};