10x 3' gene expression 5' gene expression antibody derived tags (adt) flex hashtag oligos (hto) plex quantification rna variable diversity joining (vdj)

cell_ranger_multi

Using cellranger-multi software, barcoded and probe-based libraries for gene expression assays are quantified against an index, which can be optionally created.

workflow

Steps

Create anlaysis configuration file

Write a formatted configuration file that includes all libraries in this project which will be subset for libraries in a dataset.

workflow:L68 cell_ranger_multi/make_input_csv

Quantify assays

Use the FastQ files to quantify RNA expression and additional assays in single cells.

workflow:L119 cell_ranger_multi/count

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: quantification:cell_ranger_multi:tasks.

Tag	Description
`:configuration_params`	Channel containing information of which samples and assays are in each library.
`:libraries_to_quantify`	Paths to the newly-created configuration files for each library.
`:quantified_datasets`	Parameter sets of libraries that were quantified into datasets.
`:result`	Input parameters with the `index path` (if applicable), `config_file`, `quantification method` and `quantification path` keys added.
`:tasks`	Each task’s output `task.yaml` files from the `task` channel.