Improve azimuth matrix cleaning

hubmapconsortium · Mar 26, 2024 · faaf02d · faaf02d
1 parent a005bdb
commit faaf02d
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git 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
@@ -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