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platforma-open · Aug 29, 2024 · 05f5d6a · 05f5d6a
1 parent f2e3fc6
commit 05f5d6a
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Showing 4 changed files with 41 additions and 2 deletions.
diff --git a/test/assets/expected_results/mixcr.sh b/test/assets/expected_results/mixcr.sh
@@ -1,3 +1,6 @@
 #!/bin/bash
 
+set -e
+
+mixcr exportPreset --preset-name milab-human-dna-xcr-7genes-multiplex preset.json
 mixcr analyze milab-human-dna-xcr-7genes-multiplex ../small_data_R1.fastq.gz ../small_data_R2.fastq.gz result
diff --git a/test/src/wf.test.ts b/test/src/wf.test.ts
@@ -133,6 +133,7 @@ blockTest(
       clonotypingBlockId,
       10000
     );
+
     console.dir(clonotypingStableState2, { depth: 5 });
   }
 );
diff --git a/workflow/src/mixcr-analyze.tpl.tengo b/workflow/src/mixcr-analyze.tpl.tengo
@@ -4,6 +4,7 @@ self := import("@milaboratory/tengo-sdk:tpl")
 pConstants := import("@milaboratory/tengo-sdk:pframes.constants")
 ll := import("@milaboratory/tengo-sdk:ll")
 exec := import("@milaboratory/tengo-sdk:exec")
+smart := import("@milaboratory/tengo-sdk:smart")
 
 json := import("json")
 
@@ -15,6 +16,7 @@ self.body(func(inputs) {
 	params := inputs.params
 	preset := params.preset
 	fileExtension := params.fileExtension
+	reports := params.reports
 
 	presetContent := inputs.presetContent.getDataAsJson()
 	pfconvParams := inputs.pfconvParams // already in JSON
@@ -51,10 +53,25 @@ self.body(func(inputs) {
 
 		mixcrCmdBuilder.saveFile("result.qc.json")
 
+		for report in reports {
+			mixcrCmdBuilder.saveFile(report.fileJson)
+			mixcrCmdBuilder.saveFile(report.fileTxt)
+		}
+
 		mixcrCmd := mixcrCmdBuilder.run()
 
+		reportsMap := smart.structBuilder(
+			pConstants.RTYPE_P_COLUMN_DATA_RESOURCE_MAP,
+			json.encode({ keyLength: groupKeyLength })
+		)
+		for report in reports {
+			reportsMap.createInputField(json.encode([report.id, "json"])).set(mixcrCmd.saveFile(report.fileJson))
+			reportsMap.createInputField(json.encode([report.id, "txt"])).set(mixcrCmd.saveFile(report.fileTxt))
+		}
+
 		return {
-			qc: mixcrCmd.getFile("result.qc.json")
+			qc: mixcrCmd.getFile("result.qc.json"),
+			reports: reportsMap.lockAndBuild()
 		}
 	} else {
 		ll.panic("not yet supported")

diff --git a/workflow/src/process.tpl.tengo b/workflow/src/process.tpl.tengo
@@ -23,6 +23,19 @@ self.body(func(inputs) {
 	presetContent := self.rawInputs().presetContent
 	pfconvParams := self.rawInputs().pfconvParams
 
+	reports := []
+
+	for step in presetContent.pipeline {
+		if step == "align" || step == "assemble" {
+			reports = append(reports, {
+				id: step,
+				fileJson: "result." + step + ".report.json"
+				fileTxt: "result." + step + ".report.txt"
+			})
+		}
+	}
+
+
 	if is_undefined(presetContent) {
 		ll.panic("no presetContent")
 	}
@@ -38,12 +51,17 @@ self.body(func(inputs) {
 			[{
 				type: "Resource",
 				name: "qc"
+			}, {
+				type: "ResourceMap",
+				name: "reports",
+				keyLength: 2 // [reportType, reportFormat]
 			}],
 			false,
 			{
 				params: smart.createJsonResource({
 					preset: preset,
-					fileExtension: fileExtension
+					fileExtension: fileExtension,
+					reports: reports
 				}),
 				presetContent: presetContent,
 				pfconvParams: pfconvParams
-Original file line number
+Diff line change
@@ Expand Up / @@ -133,6 +133,7 @@ blockTest( @@
           clonotypingBlockId,
         );
         console.dir(clonotypingStableState2, { depth: 5 });
       }
     );