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.
moduleInputs
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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