@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.1.1 → 2.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (17) hide show
  1. package/.turbo/turbo-build.log +1 -1
  2. package/.turbo/turbo-test.log +10 -10
  3. package/CHANGELOG.md +12 -0
  4. package/dist/tengo/lib/calculate-export-specs.lib.tengo +4 -4
  5. package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
  6. package/dist/tengo/tpl/calculate-preset-info.plj.gz +0 -0
  7. package/dist/tengo/tpl/list-presets.plj.gz +0 -0
  8. package/dist/tengo/tpl/main.plj.gz +0 -0
  9. package/dist/tengo/tpl/mixcr-analyze.plj.gz +0 -0
  10. package/dist/tengo/tpl/mixcr-export.plj.gz +0 -0
  11. package/dist/tengo/tpl/prerun.plj.gz +0 -0
  12. package/dist/tengo/tpl/process.plj.gz +0 -0
  13. package/dist/tengo/tpl/test.columns-calculate.plj.gz +0 -0
  14. package/dist/tengo/tpl/test.columns.test.plj.gz +0 -0
  15. package/package.json +2 -2
  16. package/src/calculate-export-specs.lib.tengo +4 -4
  17. package/src/process.tpl.tengo +5 -5
package/.turbo/turbo-build.log CHANGED
@@ -1,5 +1,5 @@
1
1
 
2
- > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
2
+ > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.2.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
3
3
  > rm -rf dist && pl-tengo check && pl-tengo build
4
4
 
5
5
  Processing "src/aggregate-by-clonotype-key.tpl.tengo"...
package/.turbo/turbo-test.log CHANGED
@@ -1,20 +1,20 @@
1
1
 
2
- > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.1.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
2
+ > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.2.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
3
3
  > vitest
4
4
 
5
5
 
6
6
   RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
7
7
 
8
- ✓ src/test/columns.test.ts (6 tests) 49169ms
9
- ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 13728ms
10
- ✓ checking preset for '10x-sc-xcr-vdj' 7394ms
11
- ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7337ms
12
- ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7115ms
13
- ✓ checking preset for 'rna-seq' 6700ms
14
- ✓ checking preset for 'generic-single-cell-gex' 6894ms
8
+ ✓ src/test/columns.test.ts (6 tests) 51634ms
9
+ ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 15376ms
10
+ ✓ checking preset for '10x-sc-xcr-vdj' 7604ms
11
+ ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7327ms
12
+ ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7321ms
13
+ ✓ checking preset for 'rna-seq' 6911ms
14
+ ✓ checking preset for 'generic-single-cell-gex' 7094ms
15
15
 
16
16
   Test Files  1 passed (1)
17
17
   Tests  6 passed (6)
18
-  Start at  18:50:45
19
-  Duration  49.93s (transform 43ms, setup 0ms, collect 537ms, tests 49.17s, environment 0ms, prepare 56ms)
18
+  Start at  10:25:13
19
+  Duration  52.51s (transform 50ms, setup 0ms, collect 640ms, tests 51.63s, environment 0ms, prepare 67ms)
20
20
 
package/CHANGELOG.md CHANGED
@@ -1,5 +1,17 @@
1
1
  # @platforma-open/milaboratories.mixcr-clonotyping.workflow
2
2
 
3
+ ## 2.2.1
4
+
5
+ ### Patch Changes
6
+
7
+ - 40f2800: MiXCR upgrade, higher memory limit in export
8
+
9
+ ## 2.2.0
10
+
11
+ ### Minor Changes
12
+
13
+ - 4b82d2d: Source domain for output columns changed from pl7.app/blockId to pl7.app/vdj/clonotypingRunId
14
+
3
15
  ## 2.1.1
4
16
 
5
17
  ### Patch Changes
package/dist/tengo/lib/calculate-export-specs.lib.tengo CHANGED
@@ -472,7 +472,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
472
472
  }
473
473
 
474
474
  columnsSpecPerSample = addSpec(columnsSpecPerSample, { spec: { domain: {
475
- "pl7.app/blockId": blockId
475
+ "pl7.app/vdj/clonotypingRunId": blockId
476
476
  } } })
477
477
 
478
478
 
@@ -482,10 +482,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
482
482
 
483
483
  columnsSpecPerClonotype = addSpec(columnsSpecPerClonotype, { spec: {
484
484
  domain: {
485
- "pl7.app/blockId": blockId
485
+ "pl7.app/vdj/clonotypingRunId": blockId
486
486
  },
487
487
  annotations: {
488
- "pl7.app/segmentedBy": string(json.encode(["pl7.app/blockId"]))
488
+ "pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
489
489
  }
490
490
  } })
491
491
 
@@ -567,7 +567,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
567
567
  type: "String",
568
568
  domain: {
569
569
  "pl7.app/vdj/cellTagId": tag,
570
- "pl7.app/blockId": blockId
570
+ "pl7.app/vdj/clonotypingRunId": blockId
571
571
  },
572
572
  annotations: a(orderP, true, {
573
573
  "pl7.app/label": label
package/dist/tengo/tpl/list-presets.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/main.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/mixcr-analyze.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/mixcr-export.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/prerun.plj.gz CHANGED
Binary file
package/dist/tengo/tpl/process.plj.gz CHANGED
Binary file
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
3
- "version": "2.1.1",
3
+ "version": "2.2.1",
4
4
  "description": "Tengo-based template",
5
5
  "dependencies": {
6
6
  "@platforma-open/milaboratories.mixcr-clonotyping-2.sc-clonotype-builder": "1.0.1"
@@ -10,7 +10,7 @@
10
10
  "@platforma-sdk/workflow-tengo": "^2.15.6",
11
11
  "@milaboratories/software-pframes-conv": "2.1.16",
12
12
  "@platforma-open/milaboratories.software-small-binaries": "^1.15.16",
13
- "@platforma-open/milaboratories.software-mixcr": "4.7.0-147-develop",
13
+ "@platforma-open/milaboratories.software-mixcr": "4.7.0-148-develop",
14
14
  "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
15
15
  "@platforma-sdk/test": "^1.22.100",
16
16
  "vitest": "^2.1.8",
package/src/calculate-export-specs.lib.tengo CHANGED
@@ -472,7 +472,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
472
472
  }
473
473
 
474
474
  columnsSpecPerSample = addSpec(columnsSpecPerSample, { spec: { domain: {
475
- "pl7.app/blockId": blockId
475
+ "pl7.app/vdj/clonotypingRunId": blockId
476
476
  } } })
477
477
 
478
478
  // "pl7.app/segmentedBy" annotation indicates columns that can be meaningfully merged across
@@ -482,10 +482,10 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
482
482
 
483
483
  columnsSpecPerClonotype = addSpec(columnsSpecPerClonotype, { spec: {
484
484
  domain: {
485
- "pl7.app/blockId": blockId
485
+ "pl7.app/vdj/clonotypingRunId": blockId
486
486
  },
487
487
  annotations: {
488
- "pl7.app/segmentedBy": string(json.encode(["pl7.app/blockId"]))
488
+ "pl7.app/segmentedBy": string(json.encode(["pl7.app/vdj/clonotypingRunId"]))
489
489
  }
490
490
  } })
491
491
 
@@ -567,7 +567,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
567
567
  type: "String",
568
568
  domain: {
569
569
  "pl7.app/vdj/cellTagId": tag,
570
- "pl7.app/blockId": blockId
570
+ "pl7.app/vdj/clonotypingRunId": blockId
571
571
  },
572
572
  annotations: a(orderP, true, {
573
573
  "pl7.app/label": label
package/src/process.tpl.tengo CHANGED
@@ -132,7 +132,7 @@ self.body(func(inputs) {
132
132
  valueType: "File",
133
133
  name: "mixcr.com/qc",
134
134
  domain: {
135
- "pl7.app/blockId": blockId
135
+ "pl7.app/vdj/clonotypingRunId": blockId
136
136
  }
137
137
  },
138
138
  name: "qc"
@@ -142,7 +142,7 @@ self.body(func(inputs) {
142
142
  kind: "PColumn",
143
143
  name: "pl7.app/log",
144
144
  domain: {
145
- "pl7.app/blockId": blockId
145
+ "pl7.app/vdj/clonotypingRunId": blockId
146
146
  },
147
147
  valueType: "Log"
148
148
  },
@@ -153,7 +153,7 @@ self.body(func(inputs) {
153
153
  kind: "PColumn",
154
154
  name: "mixcr.com/clns",
155
155
  domain: {
156
- "pl7.app/blockId": blockId
156
+ "pl7.app/vdj/clonotypingRunId": blockId
157
157
  },
158
158
  annotations: clnsAnnotations,
159
159
  valueType: "File"
@@ -166,7 +166,7 @@ self.body(func(inputs) {
166
166
  kind: "PColumn",
167
167
  name: "mixcr.com/report",
168
168
  domain: {
169
- "pl7.app/blockId": blockId
169
+ "pl7.app/vdj/clonotypingRunId": blockId
170
170
  },
171
171
  valueType: "File",
172
172
  axesSpec: [ {
@@ -266,7 +266,7 @@ self.body(func(inputs) {
266
266
  kind: "PColumn",
267
267
  name: "mixcr.com/clonotypeTable",
268
268
  domain: {
269
- "pl7.app/blockId": blockId
269
+ "pl7.app/vdj/clonotypingRunId": blockId
270
270
  },
271
271
  valueType: "File"
272
272
  },