integrate.yaml Reference

This configuration file corresponds to --option=integrate and defines how input data are organized for ingestion and cross-sample integration. The default values are listed below.

Parameter	Default	Description
option	integrate	Fixed identifier for the analysis stage
results_folder	results	Root directory for analysis outputs
data_fold	data	Root directory for raw input data
sample_list	sample.txt	Path to the sample list file
run_type	visium	Platform type, such as visium, visium_HD, or xenium
channel	compare_analysis	Analysis channel, either single-sample or multi-sample
cells_boundaries	False	Whether to load the cell boundary layer for Xenium
nucleus_boundaries	False	Whether to load the nucleus boundary layer for Xenium
nucleus_labels	False	Whether to load the nucleus label layer for Xenium
morphology_mip	False	Whether to load the morphology MIP image for Xenium
geojson	cell_segmentations.geojson	Segmentation filename for visium_segment
image	tissue_hires_image.png	Tissue image filename for visium_segment
scale_factors	scalefactors_json.json	Scale factor filename
coor_file	BeadLocationsForR.csv	Coordinate filename for slide_seq

Tuning suggestions

1. In most projects, you only need to modify run_type, channel, and sample_list.

2. Enable or adjust layer-related parameters only for Xenium or visium_segment data.

3. In collaborative projects, keep results_folder fixed so that downstream paths remain stable and reproducible.