seurat

Analysis of single cell data using Seurat-based methods.

Steps

Create a Seurat object

Datasets are split into two channels according to presence of the seurat file parameter. The seurat/prepare workflow for the quantification method is used to create an object.

workflow:L23

Printable channels

These channels can be dumped to the output device using the `-dump-channels` Nextflow option with the workflow root tag and the channel tag, for example: seurat:tasks.

Tag	Description
`:quantified_by.cell_ranger`	Channel of datasets for which a Seurat oject is required and was quantified by Cell Ranger.
`:quantified_by.cell_ranger_arc`	Cell Ranger ARC-qauntified datasets that do not have a `seurat file`.
`:quantified_by.unknown`	Datasets that lack both `seurat file` and `quantification method`.
`:result`	The parameters channels with workflow parameters included.
`:tasks`	Each task’s output `task.yaml` files from the `task` channel.