@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.23.3 → 3.23.4

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 (18) hide show
  1. package/.turbo/turbo-build.log +1 -1
  2. package/CHANGELOG.md +6 -0
  3. package/dist/tengo/lib/calculate-export-specs.lib.tengo +30 -6
  4. package/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz +0 -0
  5. package/dist/tengo/tpl/calculate-preset-info.plj.gz +0 -0
  6. package/dist/tengo/tpl/export-report.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-single-cell.plj.gz +0 -0
  13. package/dist/tengo/tpl/process.plj.gz +0 -0
  14. package/dist/tengo/tpl/test.columns-calculate.plj.gz +0 -0
  15. package/dist/tengo/tpl/test.columns.test.plj.gz +0 -0
  16. package/package.json +1 -1
  17. package/src/calculate-export-specs.lib.tengo +30 -6
  18. package/src/test/columns.test.ts +10 -0
package/.turbo/turbo-build.log CHANGED
@@ -1,6 +1,6 @@
1
1
   WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
2
2
 
3
- > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.3 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
3
+ > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.23.4 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
4
4
  > shx rm -rf dist && pl-tengo check && pl-tengo build
5
5
 
6
6
  info: Skipping unknown file type: test/columns.test.ts
package/CHANGELOG.md CHANGED
@@ -1,5 +1,11 @@
1
1
  # @platforma-open/milaboratories.mixcr-clonotyping.workflow
2
2
 
3
+ ## 3.23.4
4
+
5
+ ### Patch Changes
6
+
7
+ - 9c08972: Update RNA-seq preset
8
+
3
9
  ## 3.23.3
4
10
 
5
11
  ### Patch Changes
package/dist/tengo/lib/calculate-export-specs.lib.tengo CHANGED
@@ -133,6 +133,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
133
133
  ops := exportSpecOpsFromPreset(presetSpecForBack)
134
134
 
135
135
  assemblingFeature := ops.assemblingFeature
136
+ isRnaSeqPreset := is_undefined(assemblingFeature)
136
137
  cellTags := ops.cellTags
137
138
  hasUmi := ops.hasUmi
138
139
  splitByC := ops.splitByC
@@ -175,12 +176,35 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
175
176
  clonotypeKeyArgs := undefined
176
177
 
177
178
  if !is_undefined(assemblingFeature) {
178
- clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
179
- clonotypeKeyArgs = [
180
- [ "-nFeature", assemblingFeature ],
181
- [ "-vGene" ],
182
- [ "-jGene" ]
183
- ]
179
+ if isRnaSeqPreset {
180
+ clonotypeKeyColumns = [
181
+ "nSeqFR1",
182
+ "nSeqCDR1",
183
+ "nSeqFR2",
184
+ "nSeqCDR2",
185
+ "nSeqFR3",
186
+ "nSeqCDR3",
187
+ "bestVGene",
188
+ "bestJGene"
189
+ ]
190
+ clonotypeKeyArgs = [
191
+ [ "-nFeature", "FR1" ],
192
+ [ "-nFeature", "CDR1" ],
193
+ [ "-nFeature", "FR2" ],
194
+ [ "-nFeature", "CDR2" ],
195
+ [ "-nFeature", "FR3" ],
196
+ [ "-nFeature", "CDR3" ],
197
+ [ "-vGene" ],
198
+ [ "-jGene" ]
199
+ ]
200
+ } else {
201
+ clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
202
+ clonotypeKeyArgs = [
203
+ [ "-nFeature", assemblingFeature ],
204
+ [ "-vGene" ],
205
+ [ "-jGene" ]
206
+ ]
207
+ }
184
208
  if splitByC {
185
209
  clonotypeKeyColumns += ["bestCHit"]
186
210
  clonotypeKeyArgs += [ [ "-cHit" ] ]
package/dist/tengo/tpl/export-report.plj.gz CHANGED
Binary file
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": "3.23.3",
3
+ "version": "3.23.4",
4
4
  "description": "Tengo-based template",
5
5
  "dependencies": {
6
6
  "@platforma-sdk/workflow-tengo": "5.8.2",
package/src/calculate-export-specs.lib.tengo CHANGED
@@ -133,6 +133,7 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
133
133
  ops := exportSpecOpsFromPreset(presetSpecForBack)
134
134
 
135
135
  assemblingFeature := ops.assemblingFeature
136
+ isRnaSeqPreset := is_undefined(assemblingFeature)
136
137
  cellTags := ops.cellTags
137
138
  hasUmi := ops.hasUmi
138
139
  splitByC := ops.splitByC
@@ -175,12 +176,35 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId, expor
175
176
  clonotypeKeyArgs := undefined
176
177
 
177
178
  if !is_undefined(assemblingFeature) {
178
- clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
179
- clonotypeKeyArgs = [
180
- [ "-nFeature", assemblingFeature ],
181
- [ "-vGene" ],
182
- [ "-jGene" ]
183
- ]
179
+ if isRnaSeqPreset {
180
+ clonotypeKeyColumns = [
181
+ "nSeqFR1",
182
+ "nSeqCDR1",
183
+ "nSeqFR2",
184
+ "nSeqCDR2",
185
+ "nSeqFR3",
186
+ "nSeqCDR3",
187
+ "bestVGene",
188
+ "bestJGene"
189
+ ]
190
+ clonotypeKeyArgs = [
191
+ [ "-nFeature", "FR1" ],
192
+ [ "-nFeature", "CDR1" ],
193
+ [ "-nFeature", "FR2" ],
194
+ [ "-nFeature", "CDR2" ],
195
+ [ "-nFeature", "FR3" ],
196
+ [ "-nFeature", "CDR3" ],
197
+ [ "-vGene" ],
198
+ [ "-jGene" ]
199
+ ]
200
+ } else {
201
+ clonotypeKeyColumns = ["nSeq" + assemblingFeature, "bestVGene", "bestJGene"]
202
+ clonotypeKeyArgs = [
203
+ [ "-nFeature", assemblingFeature ],
204
+ [ "-vGene" ],
205
+ [ "-jGene" ]
206
+ ]
207
+ }
184
208
  if splitByC {
185
209
  clonotypeKeyColumns += ["bestCHit"]
186
210
  clonotypeKeyArgs += [ [ "-cHit" ] ]
package/src/test/columns.test.ts CHANGED
@@ -111,6 +111,16 @@ const testCases: TestCase[] = [
111
111
  expect(config.columnsSpec.find((c: any) => c.column === 'readFraction')).toBeDefined();
112
112
  expect(config.columnsSpec.find((c: any) => c.column === 'nSeqCDR3')).toBeDefined();
113
113
  expect(config.columnsSpec.find((c: any) => c.column === 'aaSeqCDR3')).toBeDefined();
114
+ expect(config.clonotypeKeyColumns).toEqual([
115
+ 'nSeqFR1',
116
+ 'nSeqCDR1',
117
+ 'nSeqFR2',
118
+ 'nSeqCDR2',
119
+ 'nSeqFR3',
120
+ 'nSeqCDR3',
121
+ 'bestVGene',
122
+ 'bestJGene'
123
+ ]);
114
124
  }
115
125
  },
116
126
  {