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Allow custom checkpoint location #406

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Allow custom checkpoint location #406

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4ed39b9
set output checkpoint according to checkpoint option
edg1983 Jan 14, 2025
e603e69
set output_checkpoint_tarball to checkpoint option value
edg1983 Jan 14, 2025
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5 changes: 5 additions & 0 deletions cellbender/remove_background/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -653,6 +653,11 @@ def run_inference(dataset_obj: SingleCellRNACountsDataset,

logger.info('No checkpoint loaded.')

# If checkpoint is not loaded set output_checkpoint_tarball to checkpoint_filename
# In this way the user can use checkpoint option to set a custom locatio for checkpoint file
output_checkpoint_tarball = args.input_checkpoint_tarball
logger.info(f'New checkpoint file will be saved as {output_checkpoint_tarball}')

# Get the trimmed count matrix (transformed if called for).
count_matrix = dataset_obj.get_count_matrix()

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