From b2bf6b450e843696e8141f650902df68a40866fe Mon Sep 17 00:00:00 2001
From: Dmitry Bolotin <bolotin.dmitriy@gmail.com>
Date: Fri, 29 Nov 2024 08:12:16 +0200
Subject: [PATCH] Fix for presets undefined assemlingFeature (i.e. rna-seq)

---
 .changeset/wild-bats-type.md   |  5 +++++
 workflow/src/process.tpl.tengo | 18 ++++++++++++++----
 2 files changed, 19 insertions(+), 4 deletions(-)
 create mode 100644 .changeset/wild-bats-type.md

diff --git a/.changeset/wild-bats-type.md b/.changeset/wild-bats-type.md
new file mode 100644
index 0000000..a697b3d
--- /dev/null
+++ b/.changeset/wild-bats-type.md
@@ -0,0 +1,5 @@
+---
+'@platforma-open/milaboratories.mixcr-clonotyping.workflow': patch
+---
+
+Fix for presets undefined assemlingFeature (i.e. rna-seq)
diff --git a/workflow/src/process.tpl.tengo b/workflow/src/process.tpl.tengo
index 8a417b2..1073235 100644
--- a/workflow/src/process.tpl.tengo
+++ b/workflow/src/process.tpl.tengo
@@ -172,13 +172,23 @@ self.body(func(inputs) {
 
 	// calculating clns annotations
 
-	clnsAnnotations := {
+	removeUndefined := func(m) {
+		r := {}
+		for k, v in m {
+			if !is_undefined(v) {
+				r[k] = v
+			}
+		}
+		return r;
+	}
+
+	clnsAnnotations := removeUndefined({
 		"mixcr.com/assemblingFeature": joinOrUndefined(presetContent.assemblingFeature),
 		"mixcr.com/cellTags": joinOrUndefined(presetContent.cellTags),
 		"mixcr.com/coveredFeaturesOnExport": joinOrUndefined(presetContent.coveredFeaturesOnExport),
 		"mixcr.com/umiTags": joinOrUndefined(presetContent.umiTags),
 		"pl7.app/label": "MiXCR Clonesets"
-	}
+	})
 	if hasAssembleContigs {
 		clnsAnnotations["mixcr.com/contigsAssembled"] = "true"
 	}
@@ -196,7 +206,7 @@ self.body(func(inputs) {
 			valueType: "File",
 			axesSpec: [
 				inputSpec.axesSpec[0]
-				]
+			]
 		}),
 		"qc.data": mixcrResults.output("qc"),
 
@@ -209,7 +219,7 @@ self.body(func(inputs) {
 			valueType: "Log",
 			axesSpec: [
 				inputSpec.axesSpec[0]
-				]
+			]
 		}),
 		"logs.data": mixcrResults.output("log"),