Sort layers alphabetically for deterministic h5ad output

The HDF5 B-tree stores group children in insertion order, and Python
set iteration order (used when populating layers from output_assays)
is non-deterministic. This caused the layers (spliced, unspliced,
ambiguous) to be written in different orders across runs, producing
different md5 checksums even though the data was identical.

Sort layers alphabetically via OrderedDict before writing h5ad files
to ensure byte-level reproducibility.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: an-altosian

src/qcatch/input_processing.py

@@ -5,6 +5,7 @@
 import logging
 import os
 import shutil
+from collections import OrderedDict
 from pathlib import Path
 
 import numpy as np
@@ -469,6 +470,9 @@ def save_results(args, version, intermediate_result, valid_bcs):
         args.input.mtx_data.obs_names.sort_values(), args.input.mtx_data.var_names.sort_values()
     ].copy()
 
+    # Sort layers alphabetically for deterministic h5ad output
+    args.input.mtx_data.layers = OrderedDict(sorted(args.input.mtx_data.layers.items()))
+
     if args.input.is_h5ad and output_dir == args.input.dir:
         # Inplace overwrite: same location as original
         temp_file = os.path.join(output_dir, "quants.h5ad")
@@ -494,6 +498,8 @@ def save_results(args, version, intermediate_result, valid_bcs):
         filter_mtx_data = filter_mtx_data[
             filter_mtx_data.obs_names.sort_values(), filter_mtx_data.var_names.sort_values()
         ].copy()
+        # Sort layers alphabetically for deterministic h5ad output
+        filter_mtx_data.layers = OrderedDict(sorted(filter_mtx_data.layers.items()))
         # Save the filtered anndata to a new file
         filter_mtx_data_filename = os.path.join(output_dir, "filtered_quants.h5ad")
         filter_mtx_data.write_h5ad(filter_mtx_data_filename, compression="gzip")