merge.yaml Reference

This configuration file corresponds to spatialsnake useful_tool --option=merge and is used for object merging and external annotation write-back.

Parameter	Default	Description
output_dir	results/useful_results	Output directory for merged results
merge_by	sample	Merge strategy, such as sample, clusters, celltype, or reannotation
reordering	False	Whether to reorder cluster labels
re_sample	False	Whether to rebuild sample names
cluster_key	clusters	Name of the clustering field
annotation_csv	""	Path to an external annotation file for the reannotation branch
csv_cell_col	Barcode	Cell ID column name in the external annotation file
csv_label_col	Grouped_Annotation	Label column name in the external annotation file
input_cell_col	cell_id	Cell ID column name in the input object
target_col	sub_celltype	Target column name for annotation write-back
original_celltype_col	celltype	Original label column used as a fallback reference

Tuning suggestions

1. For standard merging, merge_by and output_dir are usually sufficient.

2. For external annotation write-back, first verify that csv_cell_col and input_cell_col match correctly.

3. When writing back new labels, it is usually better to change target_col and preserve the original celltype column for traceability.