@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.10.1 → 2.12.0

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}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.10.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.12.0 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
   info: Skipping unknown file type: test/columns.test.ts

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}
 
-> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.10.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.12.0 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 > vitest
 
 
  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
 
- ✓ src/test/columns.test.ts (6 tests) 53265ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12934ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8419ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8256ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8191ms
-   ✓ checking preset for 'rna-seq' 7730ms
-   ✓ checking preset for 'generic-single-cell-gex' 7734ms
+ ✓ 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
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  15:22:19
-   Duration  54.10s (transform 42ms, setup 0ms, collect 592ms, tests 53.27s, environment 0ms, prepare 65ms)
+   Start at  10:21:30
+   Duration  55.25s (transform 47ms, setup 0ms, collect 610ms, tests 54.40s, environment 0ms, prepare 67ms)
 

package/CHANGELOG.md

@@ -1,5 +1,30 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.12.0
+
+### Minor Changes
+
+- 90a29d2: Fix mixcr-analyze template hash
+
+### Patch Changes
+
+- 90a29d2: SDK upgrade
+- Updated dependencies [18e0e70]
+- Updated dependencies [90a29d2]
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.hash-column@1.1.1
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts@1.1.3
+
+## 2.11.0
+
+### Minor Changes
+
+- 0db1bdf: Migration to hash-based cloonotype keys
+
+### Patch Changes
+
+- Updated dependencies [0db1bdf]
+  - @platforma-open/milaboratories.mixcr-clonotyping-2.hash-column@1.1.0
+
 ## 2.10.1
 
 ### Patch Changes

package/package.json

@@ -1,17 +1,18 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.10.1",
+  "version": "2.12.0",
   "description": "Tengo-based template",
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.1.0",
-    "@platforma-open/milaboratories.mixcr-clonotyping-2.single-cell-scripts": "1.1.2"
+    "@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"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "^2.1.0",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-150-develop",
     "@platforma-open/milaboratories.software-ptransform": "^1.3.1",
-    "@platforma-sdk/test": "^1.29.8",
-    "vitest": "^2.1.8",
+    "@platforma-sdk/test": "^1.29.17",
+    "vitest": "~2.1.8",
     "typescript": "~5.5.4"
   },
   "scripts": {

package/src/mixcr-analyze.tpl.tengo

@@ -1,3 +1,5 @@
+//tengo:hash_override D70EDB25-6FF6-4615-966D-B79B04B5751C
+
 // mixcr analyze
 
 self := import("@platforma-sdk/workflow-tengo:tpl")

package/src/mixcr-export.tpl.tengo

@@ -11,6 +11,7 @@ self.defineOutputs("tsv", "tsvForSingleCell")
 
 mixcrSw := assets.importSoftware("@platforma-open/milaboratories.software-mixcr:low-memory")
 ptransformSw := assets.importSoftware("@platforma-open/milaboratories.software-ptransform:main")
+hashColumnSw := assets.importSoftware("@platforma-open/milaboratories.mixcr-clonotyping-2.hash-column:main")
 
 self.body(func(inputs) {
 	clnsFile := inputs[pConstants.VALUE_FIELD_NAME]
@@ -75,25 +76,25 @@ self.body(func(inputs) {
 	if is_undefined(clonotypeKeyColumns) {
 		result.tsv = unprocessedTsv
 	} else {
-		// Adding clonotypeKey column
-		pWorkflow := {
-			steps: [ {
-				type: "combine_columns_as_json",
-				src: clonotypeKeyColumns,
-				dst: "clonotypeKey"
-			} ]
+		hashCmdBuilder := exec.builder().
+			printErrStreamToStdout().
+			software(hashColumnSw).
+			arg("--input-table").arg("input.tsv").
+			addFile("input.tsv", unprocessedTsv).
+			arg("--output-table").arg("output.tsv").
+			arg("--calculate")
+
+		for col in clonotypeKeyColumns {
+			hashCmdBuilder.arg(col)
 		}
 
-		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").
+		hashCmdBuilder.arg("clonotypeKey")
+
+		hashCmd := hashCmdBuilder.
+			saveFile("output.tsv").
 			run()
 
-		processedTsv := aggregateCmd.getFile("output.tsv")
+		processedTsv := hashCmd.getFile("output.tsv")
 
 		result.tsv = processedTsv
 	}
@@ -141,6 +142,33 @@ self.body(func(inputs) {
 			run()
 
 		result.tsvForSingleCell = aggregateCmd.getFile("output.tsv")
+
+		// uncomment this to use hashes
+
+		// hashCmdBuilderSingleCell := exec.builder().
+		// 	printErrStreamToStdout().
+		// 	software(hashColumnSw).
+		// 	arg("--input-table").arg("input.tsv").
+		// 	addFile("input.tsv", unprocessedTsvForSingleCell).
+		// 	arg("--output-table").arg("output.tsv")
+
+		// hashCmdBuilderSingleCell.arg("--calculate")
+		// for col in clonotypeKeyColumns {
+		// 	hashCmdBuilderSingleCell.arg(col)
+		// }
+		// hashCmdBuilderSingleCell.arg("clonotypeKey")
+
+		// hashCmdBuilderSingleCell.arg("--calculate")
+		// for col in cellTagColumns {
+		// 	hashCmdBuilderSingleCell.arg(col)
+		// }
+		// hashCmdBuilderSingleCell.arg("cellTag")
+
+		// hashCmdSingleCell := hashCmdBuilderSingleCell.
+		// 	saveFile("output.tsv").
+		// 	run()
+
+		// result.tsvForSingleCell = hashCmdSingleCell.getFile("output.tsv")
 	}
 
 	return result