Merge branch 'discvr-25.11' into 25.11_fb_jb

bbimber · web-flow · commit 87d5a2eb2c14 · 2026-02-03T13:51:09.000-08:00
diff --git a/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R b/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R
@@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-  if (! 'TRB_Segments' %in% names(seuratObj@meta.data)) {
+  if (! 'TRB_WithProductive' %in% names(seuratObj@meta.data)) {
     print('Re-running AppendTcr to add segment columns')
     seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)
   }
diff --git a/singlecell/resources/chunks/PredictTcellActivation.R b/singlecell/resources/chunks/PredictTcellActivation.R
@@ -11,6 +11,11 @@ for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
+  if (! 'TRB_WithProductive' %in% names(seuratObj@meta.data)) {
+    print('Re-running AppendTcr to add segment columns')
+    seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)
+  }
+
   toDrop <- grep(names(seuratObj@meta.data), pattern = "sPLS", value = TRUE)
   if (length(toDrop) > 0) {
     print(paste0('Dropping pre-existing columns: ', paste0(toDrop, collapse = ', ')))

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) {`
`11`	`11`	`printName(datasetId)`
`12`	`12`	`seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])`
`13`	`13`
`14`		`- if (! 'TRB_Segments' %in% names(seuratObj@meta.data)) {`
	`14`	`+ if (! 'TRB_WithProductive' %in% names(seuratObj@meta.data)) {`
`15`	`15`	`print('Re-running AppendTcr to add segment columns')`
`16`	`16`	`seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)`
`17`	`17`	`}`