From 22fd51eb7f344f267fb6cd677cdb5bb138c7af11 Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Fri, 27 Oct 2023 13:14:35 -0400 Subject: [PATCH] Fix obs join in azimuth for conflicting columns --- containers/azimuth/context/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/containers/azimuth/context/main.py b/containers/azimuth/context/main.py index 636208a..c062f34 100644 --- a/containers/azimuth/context/main.py +++ b/containers/azimuth/context/main.py @@ -68,7 +68,7 @@ def create_clean_matrix(self, matrix: anndata.AnnData): def copy_annotations( self, matrix: anndata.AnnData, annotated_matrix: anndata.AnnData ): - matrix.obs = matrix.obs.join(annotated_matrix.obs) + matrix.obs = matrix.obs.join(annotated_matrix.obs, rsuffix="_azimuth") def run_azimuth_scripts(self, matrix_path: Path, reference_data: Path): script_command = ["Rscript", "/run_azimuth.R", matrix_path, reference_data]