@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 3.2.1 → 3.4.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-clonotyping/mixcr-clonotyping/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.2.1 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@3.4.0 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: test/columns.test.ts

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 3.4.0
+
+### Minor Changes
+
+- fdd3f2f: fix tracing for single cell
+
+## 3.3.0
+
+### Minor Changes
+
+- 8cee126: min quality columns added
+
 ## 3.2.1
 
 ### Patch Changes

package/dist/tengo/lib/calculate-export-specs.lib.tengo

@@ -467,6 +467,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
+				if !isImputed && !isAminoAcid {
+					columnsSpecPerClonotypeNoAggregates += [ {
+							column: "minQual" + featureU,
+							id: "min-qual-" + featureL,
+							naRegex: "region_not_covered",
+							spec: {
+								name: "pl7.app/vdj/sequenceQuality",
+								valueType: "Int",
+								domain: {
+									"pl7.app/vdj/quality": "minQuality",
+									"pl7.app/vdj/feature": featureU
+								},
+								annotations: a(orderP - 10, false, {
+									"pl7.app/min": "0",
+									"pl7.app/max": "60",
+									"pl7.app/label": "Min quality " + featureU
+								})
+							}
+						} ]
+					exportArgs += [ [ "-minFeatureQuality", featureU ] ]
+				}
 				orderP -= 100
 
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "3.2.1",
+  "version": "3.4.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^5.0.3",

package/src/calculate-export-specs.lib.tengo

@@ -467,6 +467,27 @@ calculateExportSpecs := func(presetSpecForBack, sampleIdAxisSpec, blockId) {
 						}
 					} ]
 				exportArgs += [ [ "-" + alphabetShortMixcr + "Feature" + imputedU, featureInFrameU ] ]
+				if !isImputed && !isAminoAcid {
+					columnsSpecPerClonotypeNoAggregates += [ {
+							column: "minQual" + featureU,
+							id: "min-qual-" + featureL,
+							naRegex: "region_not_covered",
+							spec: {
+								name: "pl7.app/vdj/sequenceQuality",
+								valueType: "Int",
+								domain: {
+									"pl7.app/vdj/quality": "minQuality",
+									"pl7.app/vdj/feature": featureU
+								},
+								annotations: a(orderP - 10, false, {
+									"pl7.app/min": "0",
+									"pl7.app/max": "60",
+									"pl7.app/label": "Min quality " + featureU
+								})
+							}
+						} ]
+					exportArgs += [ [ "-minFeatureQuality", featureU ] ]
+				}
 				orderP -= 100
 
 				// Adding sequence annotation columns for assembling feature

package/src/process.tpl.tengo

@@ -384,7 +384,7 @@ self.body(func(inputs) {
 			exportOutputs,
 			{
 				// will be automatically propagated to all output specs
-				traceSteps: [{type: "milaboratories.mixcr-clonotyping.export", id: blockId + "." + chain, importance: 80, label: chainInfo.name}],
+				traceSteps: isSingleCell ? [] : [{type: "milaboratories.mixcr-clonotyping.export", id: blockId + "." + chain, importance: 80, label: chainInfo.name}],
 
 				// this will cache each individual step result for 30 minutes, even if execution of some of the steps
 				// failed or whole execution was interrupted
@@ -647,6 +647,7 @@ self.body(func(inputs) {
 				singleCellOutputs,
 				{
 					aggregate: ["pl7.app/sampleId"],
+					traceSteps: [{type: "milaboratories.mixcr-clonotyping.processSingleCell", id: blockId + "." + receptor, importance: 80, label: receptorInfo.name}],
 					extra: {
 						byCellTagB: byCellTagBData,
 						propertiesA: perChainResults[chainA].clonotypeProperties.data,