@platforma-open/milaboratories.mixcr-shm-trees.workflow 3.9.0 → 3.11.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/mixcr-shm-trees/mixcr-shm-trees/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.9.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
+> @platforma-open/milaboratories.mixcr-shm-trees.workflow@3.11.0 build /home/runner/work/mixcr-shm-trees/mixcr-shm-trees/workflow
 > rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/export-settings.lib.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,17 @@
 # @platforma-open/milaboratories.mixcr-shm-trees.workflow
 
+## 3.11.0
+
+### Minor Changes
+
+- 7abb3c7: CID Conflict adhoc
+
+## 3.10.0
+
+### Minor Changes
+
+- f9b5aed: chore: update deps
+
 ## 3.9.0
 
 ### Minor Changes

package/dist/tengo/lib/tables-aggregation.lib.tengo

@@ -70,6 +70,7 @@ ensureUniqueness := func(inputTsv, params, ...aggParams) {
         writeFile("wf.json", json.encode(aggregationWorkflow)).
         arg("input.tsv").addFile("input.tsv", inputTsv).
         arg("output.tsv").saveFile("output.tsv").
+        env("CIDADHOC", "123").
         run()
 
     return aggregateCmd.getFile("output.tsv")

package/package.json

@@ -1,22 +1,22 @@
 {
   "name": "@platforma-open/milaboratories.mixcr-shm-trees.workflow",
-  "version": "3.9.0",
+  "version": "3.11.0",
   "type": "module",
   "description": "Tengo-based template",
   "//": {
     "build": "node ./scripts/build-static.mjs src/pfconv_params.json src/pfconv_params.lib.tengo && rm -rf dist && pl-tengo check && pl-tengo build && ./create_tags.sh"
   },
   "dependencies": {
-    "@platforma-sdk/workflow-tengo": "^4.4.4"
+    "@platforma-sdk/workflow-tengo": "^4.7.1"
   },
   "devDependencies": {
-    "@platforma-sdk/tengo-builder": "^2.1.3",
+    "@platforma-sdk/tengo-builder": "^2.1.7",
     "@platforma-open/milaboratories.software-mixcr": "4.7.0-165-develop",
     "@platforma-open/milaboratories.software-mitool": "2.3.1-5-main",
     "@platforma-open/milaboratories.software-ptransform": "^1.4.3",
-    "@platforma-sdk/test": "^1.30.32",
+    "@platforma-sdk/test": "1.31.13",
     "vitest": "~2.1.8",
-    "typescript": "~5.6.3"
+    "typescript": "~5.5.4"
   },
   "scripts": {
     "build": "rm -rf dist && pl-tengo check && pl-tengo build",

package/src/mixcr-export.tpl.tengo

@@ -49,7 +49,8 @@ self.body(func(inputs) {
         inLightQueue().
         secret("MI_LICENSE", "MI_LICENSE").
         software(mixcrSw).
-        arg("exportShmTrees")
+        arg("exportShmTrees").
+        env("CIDADHOC", "123")
 
     addLibraryFile(shmTreeExportsCmdBuilder)
 
@@ -75,7 +76,8 @@ self.body(func(inputs) {
         inLightQueue().
         secret("MI_LICENSE", "MI_LICENSE").
         software(mixcrSw).
-        arg("exportShmTreesWithNodes")
+        arg("exportShmTreesWithNodes").
+        env("CIDADHOC", "123")
 
     addLibraryFile(shmTreeNodesExportsCmdBuilder)
 
@@ -103,7 +105,8 @@ self.body(func(inputs) {
 		software(mixcrSw).
         arg("exportShmTreesWithNodes").
         // don't export nodes that don't have clones
-        arg("--only-observed")
+        arg("--only-observed").
+        env("CIDADHOC", "123")
 
     addLibraryFile(shmTreeNodesWithClonesExportsCmdBuilder)
 

package/src/mixcr-shm-trees.tpl.tengo

@@ -63,7 +63,8 @@ self.body(func(inputs) {
         arg("--json-report").arg("report.json").
         saveFile("report.json").
         // template specifies where result files will be written
-        arg("--output-template").arg("alleles/{file_name}.clns")
+        arg("--output-template").arg("alleles/{file_name}.clns").
+        env("CIDADHOC", "123")
 
     addLibraryFile(allelesCmdBuilder)
 
@@ -133,7 +134,8 @@ self.body(func(inputs) {
                     arg(downsamplingParam).
                     arg("clones.clns").
                     addFile("clones.clns", entry.afterAlleles).
-                    saveFile("clones.downsampled.clns")
+                    saveFile("clones.downsampled.clns").
+                    env("CIDADHOC", "123")
                 addLibraryFile(downsamplingCmdBuilder)
                 downsamplingCmd := downsamplingCmdBuilder.run()
 
@@ -156,7 +158,8 @@ self.body(func(inputs) {
         arg("--report").arg("report.txt").
         saveFile("report.txt").
         arg("--json-report").arg("report.json").
-        saveFile("report.json")
+        saveFile("report.json").
+        env("CIDADHOC", "123")
 
     if !is_undefined(globalParams.seed) {
         shmTreesCmdBuilder.env("SEED", globalParams.seed)

package/src/soi.tpl.tengo

@@ -141,6 +141,7 @@ self.body(func(inputs) {
 		arg("--target-column").arg("query").
         arg("input.tsv").addFile("input.tsv", inputTsv).
 		arg("output.tsv").saveFile("output.tsv").
+        env("CIDADHOC", "123").
 		run()
 
 	resultCsv := searchCmd.getFile("output.tsv")
@@ -182,6 +183,7 @@ self.body(func(inputs) {
 		writeFile("wf.json", json.encode(aggregationWorkflow)).
 		arg("input.tsv").addFile("input.tsv", resultCsv).
 		arg("output.tsv").saveFile("output.tsv").
+        env("CIDADHOC", "123").
 		run()
 
 	aggregatedCsv := aggregateCmd.getFile("output.tsv")

package/src/tables-aggregation.lib.tengo

@@ -70,6 +70,7 @@ ensureUniqueness := func(inputTsv, params, ...aggParams) {
         writeFile("wf.json", json.encode(aggregationWorkflow)).
         arg("input.tsv").addFile("input.tsv", inputTsv).
         arg("output.tsv").saveFile("output.tsv").
+        env("CIDADHOC", "123").
         run()
 
     return aggregateCmd.getFile("output.tsv")