cell_ranger

Using the filtered single cell expression matrix, output from Cell Ranger, a Seurat object is prepared with little modification.

workflow

Steps

Read Cell Ranger output into assays

Read the Cell Ranger filtered_feature_bc_matrix and save the result, ready to create assay(s). Two RNA assays are created for each dataset: one using features indexed by accession and another by feature name.

workflow:L36 R/Seurat/write_10x_counts_matrices R/Seurat/make_assay

Create Seurat object

Collect the miscellaneous data and assays and create a Seurat object, saved as an RDS file.

workflow:L97 R/Seurat/make_object

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:prepare:cell_ranger:tasks.

Tag	Description
`:barcoded_matrices_to_read`	Parameters to read filtered expression matrices in both accession or name modes using.
`:barcoded_matrices`	Paths to the created matrix objects that will be used to write assays.
`:rna_assays_branched.accession`	Paths to assays created using accessions.
`:rna_assays_branched.name`	Paths to assays created using names.
`:rna_assays`	Merge of accession- and name-indexed assays.
`:objects_to_create`	Parameters used to create Seurat objects.
`:objects`	Paths to created Seurat objects.
`:result`	Input parameters with `seurat path` key added.
`:tasks`	Each task’s output `task.yaml` files from the `task` channel.