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

count

Aligns and quantifies FastQ files from a multiomic 10x experiment against a reference genome and include VDJ-B/T and cell surface markers. Output matrices for gene expression and features are provided in triplet and h5 formats. VDJ data are provided separately.

module

Inputs

Channel name	Description	Type
`opt`	A map of task-specific variables.	`map`
`output dir`	A path to use as the Cell Ranger multi output directory.	`string`
`dataset_ids`	An array of datasets that should be in the library, there may be only one. When there is only one sample in the `per_sample_outs`, the sample is renamed to the hyphen-joined list of dataset IDs.	`strings`
`config.csv`	Path to the configuration file.	`file`

Outputs

Emission name	Description	Type	Filename pattern
`opt`	A map of task-specific variables.	`map`
`task`	YAML-formatted file of task parameters and software versions used by the task.	`file`	`task.yaml`
`config_csv`	Configuration file used by the task.	`file`	`*/config.csv`
`multi_quantification_path`	Cell Ranger multi outputs directory.	`path`	`*/multi`
`per_sample_quantification_path`	Cell Ranger multi gene expression outputs directory for each dataset. Subdirecotries of these include “count” and “vdj_b” for example.	`path`	`*/per_sample_outs`

Tools

cell ranger extcount multithreaded

Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

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