@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.2.1 → 3.3.0

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/CHANGELOG.md +6 -0
  3. package/dist/tengo/lib/calculate-export-specs.lib.tengo +21 -0
  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 +21 -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@3.2.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
3
+ > @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.3.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
4
4
  > 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
+ ## 3.3.0
4
+
5
+ ### Minor Changes
6
+
7
+ - 8cee126: min quality columns added
8
+
3
9
  ## 3.2.1
4
10
 
5
11
  ### Patch Changes
package/dist/tengo/lib/calculate-export-specs.lib.tengo CHANGED
@@ -467,6 +467,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
467
467
  }
468
468
  } ]
469
469
  exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
470
+ if !isImputed && !isAminoAcid {
471
+ columnsSpecPerClonotypeNoAggregates += [ {
472
+ column: "minQual" + featureU,
473
+ id: "min-qual-" + featureL,
474
+ naRegex: "region_not_covered",
475
+ spec: {
476
+ name: "pl7.app/vdj/sequenceQuality",
477
+ valueType: "Int",
478
+ domain: {
479
+ "pl7.app/vdj/quality": "minQuality",
480
+ "pl7.app/vdj/feature": featureU
481
+ },
482
+ annotations: a(orderP - 10, false, {
483
+ "pl7.app/min": "0",
484
+ "pl7.app/max": "60",
485
+ "pl7.app/label": "Min quality " + featureU
486
+ })
487
+ }
488
+ } ]
489
+ exportArgs += [ [ "-minFeatureQuality", featureU ] ]
490
+ }
470
491
  orderP -= 100
471
492
 
472
493
 
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": "3.2.1",
3
+ "version": "3.3.0",
4
4
  "description": "Tengo-based template",
5
5
  "dependencies": {
6
6
  "@platforma-sdk/workflow-tengo": "^5.0.3",
package/src/calculate-export-specs.lib.tengo CHANGED
@@ -467,6 +467,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
467
467
  }
468
468
  } ]
469
469
  exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
470
+ if !isImputed && !isAminoAcid {
471
+ columnsSpecPerClonotypeNoAggregates += [ {
472
+ column: "minQual" + featureU,
473
+ id: "min-qual-" + featureL,
474
+ naRegex: "region_not_covered",
475
+ spec: {
476
+ name: "pl7.app/vdj/sequenceQuality",
477
+ valueType: "Int",
478
+ domain: {
479
+ "pl7.app/vdj/quality": "minQuality",
480
+ "pl7.app/vdj/feature": featureU
481
+ },
482
+ annotations: a(orderP - 10, false, {
483
+ "pl7.app/min": "0",
484
+ "pl7.app/max": "60",
485
+ "pl7.app/label": "Min quality " + featureU
486
+ })
487
+ }
488
+ } ]
489
+ exportArgs += [ [ "-minFeatureQuality", featureU ] ]
490
+ }
470
491
  orderP -= 100
471
492
 
472
493
  // Adding sequence annotation columns for assembling feature