@platforma-open/milaboratories.top-antibodies.workflow 2.0.0 → 2.1.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.top-antibodies.workflow@2.0.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
+> @platforma-open/milaboratories.top-antibodies.workflow@2.1.0 build /home/runner/work/antibody-tcr-lead-selection/antibody-tcr-lead-selection/workflow
 > shx rm -rf dist && pl-tengo check && pl-tengo build
 
 Processing "src/assembling-fasta.tpl.tengo"...

package/CHANGELOG.md

@@ -1,5 +1,22 @@
 # @platforma-open/milaboratories.top-antibodies.workflow
 
+## 2.1.0
+
+### Minor Changes
+
+- 84a7fe5: Deal with ANARCI numbering issues
+
+### Patch Changes
+
+- Updated dependencies [84a7fe5]
+  - @platforma-open/milaboratories.top-antibodies.anarci-kabat@1.4.0
+
+## 2.0.1
+
+### Patch Changes
+
+- 140ce30: Support custom block label
+
 ## 2.0.0
 
 ### Major Changes

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.top-antibodies.workflow",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "type": "module",
   "description": "Block Workflow",
   "dependencies": {
@@ -8,9 +8,9 @@
     "@platforma-open/milaboratories.software-anarci": "^0.0.3",
     "@platforma-open/milaboratories.top-antibodies.sample-clonotypes": "2.0.0",
     "@platforma-open/milaboratories.top-antibodies.umap": "1.2.1",
+    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1",
     "@platforma-open/milaboratories.top-antibodies.assembling-fasta": "1.3.0",
-    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.3.0",
-    "@platforma-open/milaboratories.top-antibodies.spectratype": "1.8.1"
+    "@platforma-open/milaboratories.top-antibodies.anarci-kabat": "1.4.0"
   },
   "devDependencies": {
     "@platforma-sdk/tengo-builder": "2.4.18"

package/src/assembling-fasta.tpl.tengo

@@ -6,7 +6,7 @@ pt := import("@platforma-sdk/workflow-tengo:pt")
 pframes := import("@platforma-sdk/workflow-tengo:pframes")
 anarciSw := assets.importSoftware("@platforma-open/milaboratories.software-anarci:main")
 
-self.defineOutputs("kabat")
+self.defineOutputs("kabat", "kabatStats")
 
 self.body(func(inputs) {
 
@@ -37,13 +37,17 @@ self.body(func(inputs) {
     
     anarciFileNameBulk := "anarci.csv_" + bulkChain + ".csv"
     
+    // Pre-create empty CSV placeholders so that saveFile always finds the files,
+    // even when ANARCI cannot number any sequences (e.g. heavily engineered scaffolds)
      anarciBuilder := exec.builder().
         software(anarciSw).
         arg("-i").arg("assembling.fasta").
         arg("--scheme").arg("kabat").
         arg("--ncpu").argWithVar("{system.cpu}").
         arg("-o").arg("anarci.csv").arg("--csv").
-        addFile("assembling.fasta", cmd.getFile("assembling.fasta"))
+        addFile("assembling.fasta", cmd.getFile("assembling.fasta")).
+        writeFile("anarci.csv_H.csv", "Id\n").
+        writeFile("anarci.csv_KL.csv", "Id\n")
     if isSingleCell {
         anarciBuilder = anarciBuilder.saveFile("anarci.csv_H.csv").saveFile("anarci.csv_KL.csv")
     } else {
@@ -73,16 +77,16 @@ self.body(func(inputs) {
     }
     kabatExec = kabatExec.
         arg("--out_tsv").arg("kabat.tsv").
+        arg("--numbered_count_file").arg("numbered_count.txt").
         saveFile("kabat.tsv").
+        saveFileContent("numbered_count.txt").
         printErrStreamToStdout().
         cache(24 * 60 * 60 * 1000).
         run()
-    
-    kabat := kabatExec.getFile("kabat.tsv")
 
     return {
-        kabat: kabat
-      //  kabatPf: pframes.exportFrame(kabatDf)
+        kabat: kabatExec.getFile("kabat.tsv"),
+        kabatStats: kabatExec.getFileContent("numbered_count.txt")
     }
 })
 

package/src/filter-and-sample.tpl.tengo

@@ -105,6 +105,10 @@ self.body(func(inputs) {
     if is_undefined(traceLabel) || traceLabel == "" {
         traceLabel = "Selected Leads"
     }
+    customBlockLabel := inputs.customBlockLabel
+    if !is_undefined(customBlockLabel) && customBlockLabel != "" {
+        traceLabel = customBlockLabel + " / " + traceLabel
+    }
     trace := pSpec.makeTrace(datasetSpec,
         {
             type: "milaboratories.antibody-tcr-lead-selection",

package/src/main.tpl.tengo

@@ -164,7 +164,8 @@ wf.body(func(args) {
                 datasetSpec: datasetSpec,
                 topClonotypes: args.topClonotypes,
                 diversificationColumn: clusterColumnHeader,
-                filterTraceLabel: filterTraceLabel
+                filterTraceLabel: filterTraceLabel,
+                customBlockLabel: args.customBlockLabel
             })
 
             // Get the filtered clonotypes from the template result
@@ -245,6 +246,7 @@ wf.body(func(args) {
                 // Convert kabat.tsv to PFrame with proper specs (bulk: select heavy/light)
                 kabatPf := xsv.importFile(kabatFile, "tsv", kabatConv.getColumns(datasetSpec, featName, bulkChain), {cpu: 1, mem: "8GiB"})
                 outputs["assemblingKabatPf"] = pframes.exportFrame(kabatPf)
+                outputs["kabatStatsContent"] = assem.output("kabatStats")
             }
         }
     }