cell_num¶

Purpose¶

Computes or forwards spot-level cell number information used in spot genotype inference.

Upstream¶

• cluster
• umi_combine

Required inputs¶

• in_filter_bam
• cluster information from config/context
• sequence_type and optional bins

Input interpretation¶

Input key	Source	Required	Interpretation
in_filter_bam	bam_processing output	Yes	Filtered BAM used to estimate or validate spot-level cell support.
cluster	cluster step output/file	Yes	Spot grouping used for cell-number modeling context.
sequence_type	top-level config	Yes	Controls mode-specific behavior (Visium vs non-Visium).
bins (bin_size)	top-level config	Conditional	Used in non-Visium/binned workflows when applicable.

Parameters¶

This step is mostly controlled by:

• steps.cell_number (integer or file path)
• 0: compute from BAM/UMI profiles
• positive integer: use constant
• file path: use provided table

Parameter interpretation¶

Parameter	Type	Typical/default	Interpretation
steps.cell_number	int/path/null	unset or 0	Main mode switch: compute, fixed value, or passthrough external table.

Outputs¶

• cell_num key
• generated file: output_dir/refined_umi_read_cellNum.txt, or
• passthrough integer/path from config

Tuning notes¶

• If cell number is already known, pass it directly to avoid recomputation.