Description

Module to use Cell Ranger’s pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

gex_fastqs (file)

FASTQ files for gene expression analysis

*.fastq.gz

vdj_fastqs (file)

FASTQ files for V(D)J immunoprofiling analysis

*.fastq.gz

ab_fastqs (file)

FASTQ files for antibody analysis

*.fastq.gz

beam_fastqs (file)

FASTQ files for Barcode-Enabled Antigen Mapping (antigen analysis)

*.fastq.gz

cmo_fastqs (file)

FASTQ files for cell multiplexing data

*.fastq.gz

gex_reference (directory)

Folder containing Cellranger gene expression reference. Can also be a gzipped tarball

*.tar.gz

gex_frna_probeset (file)

Fixed RNA profiling information containing custom probes in CSV format

*.csv

gex_targetpanel (file)

Declaration of the target panel for Targeted Gene Expression analysis

*.csv

vdj_reference (directory)

Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball

*.tar.gz

vdj_primer_index (file)

List of custom V(D)J inner enrichment primers

*.csv

fb_reference (file)

The Feature Barcodes used for reference in Feature Barcoding Analysis

*.csv

beam_antigen_panel (file)

The BEAM manifest in Feature Barcode CSV format

*.csv

beam_control_panel (file)

The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format

*.csv

cmo_reference (file)

Path to a custom Cell Multiplexing CSV reference IDs, or the cmo-set option in Cellranger

*.csv

cmo_barcodes (file)

A CSV file appended to the Cellranger multi config linking samples to CMO IDs

*.csv

cmo_barcode_assignment (file)

A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis

*.csv

frna_sampleinfo (file)

Sample information for fixed RNA analysis

*.csv

Output

Name (Type)
Description
Pattern

config (file)

The resolved Cellranger multi config used for analysis

cellranger_multi_config.csv

outs (file)

Files containing the outputs of Cell Ranger

${meta.id}/outs/*

versions (file)

File containing software versions

versions.yml
included in
scrnaseq
maintainer
Github user klkeys
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Tools

cellranger
10X Genomics EULA

Cell Ranger by 10x Genomics 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.

support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp