@platforma-open/milaboratories.mixcr-clonotyping-2.workflow 2.6.1 → 2.8.0

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@2.6.1 build /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.0 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@2.6.1 test /home/runner/work/mixcr-clonotyping-2/mixcr-clonotyping-2/workflow
+> @platforma-open/milaboratories.mixcr-clonotyping-2.workflow@2.8.0 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) 55868ms
-   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 14243ms
-   ✓ checking preset for '10x-sc-xcr-vdj' 8794ms
-   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8380ms
-   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8294ms
-   ✓ checking preset for 'rna-seq' 7887ms
-   ✓ checking preset for 'generic-single-cell-gex' 8268ms
+ ✓ src/test/columns.test.ts (6 tests) 54112ms
+   ✓ checking preset for 'milab-human-dna-xcr-7genes-multiplex' 12976ms
+   ✓ checking preset for '10x-sc-xcr-vdj' 8593ms
+   ✓ checking preset for 'cellecta-human-rna-xcr-umi-drivermap-…' 8350ms
+   ✓ checking preset for 'takara-human-rna-bcr-umi-smartseq' 8290ms
+   ✓ checking preset for 'rna-seq' 7833ms
+   ✓ checking preset for 'generic-single-cell-gex' 8069ms
 
  Test Files  1 passed (1)
       Tests  6 passed (6)
-   Start at  16:45:12
-   Duration  56.68s (transform 41ms, setup 0ms, collect 572ms, tests 55.87s, environment 0ms, prepare 60ms)
+   Start at  15:43:44
+   Duration  55.17s (transform 63ms, setup 0ms, collect 737ms, tests 54.11s, environment 0ms, prepare 92ms)
 

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-clonotyping.workflow
 
+## 2.8.0
+
+### Minor Changes
+
+- 22a4bd4: passing library into exportClones template
+
+## 2.7.0
+
+### Minor Changes
+
+- a3d8933: ampliseq preset bug correction
+
 ## 2.6.1
 
 ### Patch Changes

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

@@ -46,7 +46,7 @@ assemblingFeatureInfo := func(assemblingFeature) {
 		splittedFeature := text.split(assemblingFeature, "_TO_")
 		if len(splittedFeature) == 2 {
 			if splittedFeature[1] == "FR4" {
-				productiveFeature = "{"+splittedFeature[0] + "Begin:FR4End(-1)}"
+				productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
 				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
 				coreJFeature = "FR4"
 			} else {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-clonotyping-2.workflow",
-  "version": "2.6.1",
+  "version": "2.8.0",
   "description": "Tengo-based template",
   "dependencies": {
     "@platforma-sdk/workflow-tengo": "^4.0.3",

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

@@ -46,7 +46,7 @@ assemblingFeatureInfo := func(assemblingFeature) {
 		splittedFeature := text.split(assemblingFeature, "_TO_")
 		if len(splittedFeature) == 2 {
 			if splittedFeature[1] == "FR4" {
-				productiveFeature = "{"+splittedFeature[0] + "Begin:FR4End(-1)}"
+				productiveFeature = splittedFeature[0] + "_TO_FR4(0,-1)"
 				coreVFeature = "{"+splittedFeature[0]+"Begin:FR3End}"
 				coreJFeature = "FR4"
 			} else {

package/src/mixcr-export.tpl.tengo

@@ -16,6 +16,8 @@ self.body(func(inputs) {
 	clnsFile := inputs[pConstants.VALUE_FIELD_NAME]
 
 	params := inputs.params
+	library := inputs.library
+	isLibraryFileGzipped := params.isLibraryFileGzipped
 	chains := params.chains
 	exportArgs := params.exportArgs
 
@@ -37,6 +39,14 @@ self.body(func(inputs) {
 			arg("--reset-export-clone-table-splitting").
 			arg("--chains").arg(chains)
 
+		if library {
+			if isLibraryFileGzipped {
+				mixcrCmdBuilder.addFile("library.json.gz", library)
+			} else {
+				mixcrCmdBuilder.addFile("library.json", library)
+			}
+		}
+
 		additionalAction(mixcrCmdBuilder)
 
 		return mixcrCmdBuilder.

package/src/process.tpl.tengo

@@ -351,8 +351,10 @@ self.body(func(inputs) {
 						clonotypeKeyColumns: clonotypeKeyColumns,
 						clonotypeKeyArgs: clonotypeKeyArgs,
 						cellTagColumns: cellTagColumns,
-						exportArgs: exportArgs
-					}
+						exportArgs: exportArgs,
+						isLibraryFileGzipped: isLibraryFileGzipped
+					},
+					library: library
 				}
 			}
 		)