Seurat v3[1] introduced new methods for the integration of multiple single-cell datasets, no matter whether they were collected from different individuals, experimental conditions, technologies, etc. Seurat 3 integration method aims to first identify 'anchors' between pairs of datasets. These 'anchors' are then used to harmonize the datasets. Its standard workflow use a subset of the data as reference for the integrate analysis. The method integrates all other data with the reference subset. The subset can be one sample or a subgroup of samples defined by the factor attribute. Its "Standard Workflow" is provided in Partek Flow.

Seurat3 integration in Flow can be invoked in Batch removal section if a Normalized counts data node is selected (Figure 1). We do not recommend performing this integration on SCTransform output data node. 

Figure 1. Seurat3 integration task in Batch removal section in Flow.

...