From 2d3d30fda0752d2aa998dbfa9e8365e97ab065e9 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Thu, 25 Apr 2024 10:03:35 -0500
Subject: [PATCH] make sure has_celltypes is in supplemental

---
 templates/qc_report/celltypes_supplemental_report.rmd | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/templates/qc_report/celltypes_supplemental_report.rmd b/templates/qc_report/celltypes_supplemental_report.rmd
index 4b1dc159..03e3b3c0 100644
--- a/templates/qc_report/celltypes_supplemental_report.rmd
+++ b/templates/qc_report/celltypes_supplemental_report.rmd
@@ -264,6 +264,9 @@ has_cellassign <- "cellassign" %in% metadata(processed_sce)$celltype_methods
 has_submitter <- "submitter" %in% metadata(processed_sce)$celltype_methods &&
   !all(is.na(processed_sce$submitter_celltype_annotation)) # make sure they aren't all NA
 
+# If at least 1 is present, we have cell type annotations.
+has_celltypes <- any(has_singler, has_cellassign, has_submitter)
+
 # check for umap and clusters
 has_umap <- "UMAP" %in% reducedDimNames(processed_sce)
 has_clusters <- "cluster" %in% names(colData(processed_sce))