@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.14.2 → 2.15.1

package/.test_auth.json

@@ -0,0 +1 @@
+{"conf":{"address":"http://127.0.0.1:6345","test_user":"test-user","test_password":"test-password"},"authInformation":{"jwtToken":"eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ1c2VyIjp7ImxvZ2luIjoidGVzdC11c2VyIn0sImV4cCI6MTc0NjU2MjQ5MywiaWF0IjoxNzQ1OTU3NjkzfQ.ZMQGoZ3Z2SanN_ZOemm_xqZSD7YNnYC561qeU_fU2CA"},"expiration":1746044093000}

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@2.14.2 build /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.15.1 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/.turbo/turbo-test.log

@@ -1,21 +1,21 @@
  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@2.14.2 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.15.1 test /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 > vitest
 
 
  RUN  v2.1.8 /home/runner/work/mixcr-clonotyping/mixcr-clonotyping/workflow
 
- ✓ src/test/columns.test.ts (6 tests) 53783ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 13009ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8376ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8245ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8167ms
-   ✓ checking preset for 'rna-seq' 7998ms
-   ✓ checking preset for 'generic-single-cell-gex' 7987ms
+ ✓ src/test/columns.test.ts (6 tests) 52243ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12711ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8250ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 7810ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 7940ms
+   ✓ checking preset for 'rna-seq' 7563ms
+   ✓ checking preset for 'generic-single-cell-gex' 7968ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  08:20:54
-   Duration  54.58s (transform 43ms, setup 0ms, collect 565ms, tests 53.78s, environment 0ms, prepare 59ms)
+   Start at  20:14:53
+   Duration  53.03s (transform 43ms, setup 0ms, collect 561ms, tests 52.24s, environment 0ms, prepare 60ms)
 

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.15.1
+
+### Patch Changes
+
+- 1c2dc52: Add --force-overwrite option to avoid rare bug
+
+## 2.15.0
+
+### Minor Changes
+
+- 20cd6f5: Exporting library if provided as file & attaching libraryId to clns output spec
+
 ## 2.14.2
 
 ### Patch Changes

package/package.json

@@ -1,11 +1,11 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.14.2",
+  "version": "2.15.1",
   "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",

package/src/main.tpl.tengo

@@ -59,16 +59,19 @@ wf.body(func(args) {
 	isLibraryFileGzipped := false
 
 	library := false
+	libraryId := undefined
 	species := args.species
 	libraryImportHandle := undefined
 	if !is_undefined(args.resolvedLibraryInput) {
 		library = args.resolvedLibraryInput.data
+		libraryId = args.resolvedLibraryInput.spec["domain"]["pl7.app/vdj/libraryId"]
 		librarySpec := args.resolvedLibraryInput.spec
 		species = librarySpec["annotations"]["pl7.app/species"]
 	} else if !is_undefined(args.libraryFile) {
 		fImport := file.importFile(args.libraryFile)
 		libraryImportHandle = fImport.handle
 		library = fImport.file
+		libraryId = blockId
 		species = args.customSpecies
 		isLibraryFileGzipped = args.isLibraryFileGzipped
 	}
@@ -110,6 +113,7 @@ wf.body(func(args) {
 			receptorsOrChains: receptorsOrChains,
 			limitInput: limitInput,
 			blockId: blockId,
+			libraryId: libraryId,
 			presetCommonName: args.presetCommonName,
 			isLibraryFileGzipped: isLibraryFileGzipped
 		})
@@ -131,6 +135,26 @@ wf.body(func(args) {
 		}
 	}
 
+	if !is_undefined(args.libraryFile) {
+		// If library file is provided, we need to exported it for native mixcr blocks to use it (i.e. SHM trees)
+		exports.library = {
+			data: library,
+			spec: {
+				kind: "File",
+				name: "pl7.app/vdj/library",
+				domain: {
+					"pl7.app/vdj/libraryId": libraryId // == blockId
+				},
+				annotations: {
+					"pl7.app/species": species,
+					"pl7.app/vdj/isLibrary": "true",
+					"pl7.app/vdj/libraryFormat": (isLibraryFileGzipped ? "repseqio.json.gz" : "repseqio.json"),
+					"pl7.app/label": "Library from MiXCR Clonotyping"
+				}
+			}
+	 	}
+	}
+
 	outputs := {
 		qc: pframes.exportColumnData(runMixcr.output("qc.data")),
 		reports: pframes.exportColumnData(runMixcr.output("reports.data")),

package/src/mixcr-analyze.tpl.tengo

@@ -143,6 +143,7 @@ self.body(func(inputs) {
 	}
 
 	mixcrCmdBuilder.arg("result")
+	mixcrCmdBuilder.arg("--force-overwrite")
 
 	mixcrCmdBuilder.saveFile("result.qc.json")
 	mixcrCmdBuilder.saveFile(clnsFileName)

package/src/process.tpl.tengo

@@ -62,6 +62,7 @@ self.body(func(inputs) {
 	receptorsOrChains := params.receptorsOrChains
 	limitInput := params.limitInput
 	blockId := params.blockId
+	libraryId := params.libraryId
 	presetCommonName := params.presetCommonName
 	isLibraryFileGzipped := params.isLibraryFileGzipped
 
@@ -120,6 +121,9 @@ self.body(func(inputs) {
 		"mixcr.com/umiTags": joinOrUndefined(presetSpecForBack.umiTags),
 		"pl7.app/label": "MiXCR Clonesets"
 	})
+	if libraryId {
+		clnsAnnotations["pl7.app/vdj/libraryId"] = libraryId
+	}
 	if hasAssembleContigs {
 		clnsAnnotations["mixcr.com/contigsAssembled"] = "true"
 	}