@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.12.0 → 2.14.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
- WARN  Issue while reading "/home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+ 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@2.12.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.0 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
@@ -19,17 +19,17 @@ Processing "src/test/columns.test.tpl.tengo"...
 No syntax errors found.
   info: Skipping unknown file type: test/columns.test.ts
   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-single-cell.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:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/lib/calculate-export-specs.lib.tengo
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/aggregate-by-clonotype-key.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/calculate-preset-info.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/list-presets.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/mixcr-analyze.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/mixcr-export.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/prerun.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/process-single-cell.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/process.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/test.columns-calculate.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/test.columns.test.plj.gz
+  info:   - writing /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow/dist/tengo/tpl/main.plj.gz
   info: Template Pack build done.
   info: Template Pack build done.

package/.turbo/turbo-test.log

@@ -1,21 +1,21 @@
- WARN  Issue while reading "/home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+ 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@2.12.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.14.0 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > vitest
 
 
- RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+ RUN  v2.1.8 /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 
- ✓ src/test/columns.test.ts (6 tests) 54404ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12330ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8645ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8791ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8369ms
-   ✓ checking preset for 'rna-seq' 7949ms
-   ✓ checking preset for 'generic-single-cell-gex' 8319ms
+ ✓ src/test/columns.test.ts (6 tests) 52804ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12471ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8426ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8251ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7970ms
+   ✓ checking preset for 'rna-seq' 7931ms
+   ✓ checking preset for 'generic-single-cell-gex' 7754ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  10:21:30
-   Duration  55.25s (transform 47ms, setup 0ms, collect 610ms, tests 54.40s, environment 0ms, prepare 67ms)
+   Start at  14:04:47
+   Duration  53.61s (transform 42ms, setup 0ms, collect 573ms, tests 52.80s, environment 0ms, prepare 63ms)
 

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.14.0
+
+### Minor Changes
+
+- dc86a17: single cell export and removing columns for secondary clones except CDR3 aa
+
+## 2.13.0
+
+### Minor Changes
+
+- b1f6427: species added, visibility of chain columns set to optional, mixcr updated to 4.7.0-164-develop
+
 ## 2.12.0
 
 ### Minor Changes

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

@@ -568,7 +568,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			spec: {
 				valueType: "String",
 				name: "pl7.app/vdj/chain",
-				annotations: a(orderP, true, {
+				annotations: a(orderP, false, {
 					"pl7.app/label": "Chain",
 					"pl7.app/isDiscreteFilter": "true",
 					"pl7.app/discreteValues": "['TRA','TRB','TRG','TRD','IGH','IGK','IGL']"

package/package.json

@@ -1,15 +1,15 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.12.0",
+  "version": "2.14.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^4.1.2",
-    "@platforma-open/milaboratories.mixcr-clonotyping-2.hash-column": "1.1.1",
-    "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.3"
+    "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.3",
+    "@platforma-open/milaboratories.mixcr-clonotyping-2.hash-column": "1.1.1"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.0",
-    "@platforma-open/milaboratories.software-mixcr": "4.7.0-150-develop",
+    "@platforma-open/milaboratories.software-mixcr": "4.7.0-164-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
     "@platforma-sdk/test": "^1.29.17",
     "vitest": "~2.1.8",

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

@@ -568,7 +568,7 @@ calculateExportSpecs := func(presetSpecForBack, blockId) {
 			spec: {
 				valueType: "String",
 				name: "pl7.app/vdj/chain",
-				annotations: a(orderP, true, {
+				annotations: a(orderP, false, {
 					"pl7.app/label": "Chain",
 					"pl7.app/isDiscreteFilter": "true",
 					"pl7.app/discreteValues": "['TRA','TRB','TRG','TRD','IGH','IGK','IGL']"

package/src/mixcr-export.tpl.tengo

@@ -75,7 +75,8 @@ self.body(func(inputs) {
 
 	if is_undefined(clonotypeKeyColumns) {
 		result.tsv = unprocessedTsv
-	} else {
+		
+	} else if is_undefined(cellTagColumns) {
 		hashCmdBuilder := exec.builder().
 			printErrStreamToStdout().
 			software(hashColumnSw).
@@ -96,6 +97,28 @@ self.body(func(inputs) {
 
 		processedTsv := hashCmd.getFile("output.tsv")
 
+		result.tsv = processedTsv
+
+	} else {
+		pWorkflow := {
+			steps: [ {
+				type: "combine_columns_as_json",
+				src: clonotypeKeyColumns,
+				dst: "clonotypeKey"
+			} ]
+		}
+
+		aggregateCmd := exec.builder().
+			printErrStreamToStdout().
+			software(ptransformSw).
+			arg("--workflow").arg("wf.json").
+			writeFile("wf.json", json.encode(pWorkflow)).
+			arg("input.tsv").addFile("input.tsv", unprocessedTsv).
+			arg("output.tsv").saveFile("output.tsv").
+			run()
+
+		processedTsv := aggregateCmd.getFile("output.tsv")
+
 		result.tsv = processedTsv
 	}
 

package/src/process.tpl.tengo

@@ -472,6 +472,13 @@ self.body(func(inputs) {
 				path: ["clonotypeTsv"]
 			} ]
 
+			//removing columns from secondary chain except aaSeqCDR3
+			columnsSpecPerClonotypeSecondary := []
+			for col in columnsSpecPerClonotype {
+				if col.column == "aaSeqCDR3" {
+					columnsSpecPerClonotypeSecondary += [ col ]
+				}
+			}
 			for chainIdx in [0, 1] {
 				// "A" chain is always the one that is more diverse
 				chainLetterU := ["A", "B"][chainIdx]
@@ -517,7 +524,7 @@ self.body(func(inputs) {
 						xsvType: "tsv",
 						settings: {
 							axes: axesByScClonotypeKeyWithReceptor,
-							columns: transformSpecs(columnsSpecPerClonotype, {
+							columns: transformSpecs(isPrimary ? columnsSpecPerClonotype : columnsSpecPerClonotypeSecondary, {
 								spec: {
 									domain: {
 										"pl7.app/vdj/scClonotypeChain": chainLetterU,