From faaf02d9c4b1417c5f2c0416921f450c0bb93b44 Mon Sep 17 00:00:00 2001 From: Daniel Bolin Date: Tue, 26 Mar 2024 17:04:19 -0400 Subject: [PATCH] Improve azimuth matrix cleaning --- containers/azimuth/context/main.py | 5 +++++ containers/azimuth/context/run_azimuth.R | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/containers/azimuth/context/main.py b/containers/azimuth/context/main.py index df51afd..e3a67f0 100644 --- a/containers/azimuth/context/main.py +++ b/containers/azimuth/context/main.py @@ -87,6 +87,11 @@ def create_clean_matrix( clean_obs = pandas.DataFrame(index=temp_index) clean_matrix = matrix.copy() clean_matrix.obs = clean_obs + clean_matrix.obsm = None + clean_matrix.obsp = None + clean_matrix.varm = None + clean_matrix.varp = None + clean_matrix.uns = {} return clean_matrix diff --git a/containers/azimuth/context/run_azimuth.R b/containers/azimuth/context/run_azimuth.R index 5d247c3..ce02453 100644 --- a/containers/azimuth/context/run_azimuth.R +++ b/containers/azimuth/context/run_azimuth.R @@ -9,7 +9,7 @@ matrix_path <- args[1] reference <- args[2] # Annotate -options(timeout=60 * 60) +options(timeout=10 * 60) output_data <- RunAzimuth(matrix_path, reference=reference) # Save and convert to h5ad