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:false ]

meta2

:map

Groovy Map containing sample information

gex_fastqs

:file

FASTQ files

*.fastq.gz

gex_options

:map

Optional Cell Ranger gene expression section options as a Map. Supported keys: filter-probes, r1-length, r2-length, chemistry, expect-cells, force-cells, no-secondary, check-library-compatibility, no-target-umi-filter, include-introns, create-bam (defaults to true if not set).

meta3

:map

Groovy Map containing sample information

vdj_fastqs

:file

V(D)J FASTQ files, with the chain type auto-detected by Cell Ranger (feature type VDJ)

*.fastq.gz

vdj_options

:map

Optional Cell Ranger VDJ section options as a Map. Supported keys: r1-length, r2-length. All V(D)J libraries share a single [vdj] section, so only the options of the first V(D)J library present (in the order vdj, vdj_t, vdj_t_gd, vdj_b) are used.

meta4

:map

Groovy Map containing sample information

ab_fastqs

:file

FASTQ files

*.fastq.gz

ab_options

:map

Optional Cell Ranger feature section options for Antibody Capture as a Map. Pass null to disable this modality. Supported keys: r1-length, r2-length.

meta5

:map

Groovy Map containing sample information

beam_fastqs

:file

FASTQ files

*.fastq.gz

beam_options

:map

Optional Cell Ranger BEAM section options as a Map. Reserved for future use.

meta6

:map

Groovy Map containing sample information

cmo_fastqs

:file

FASTQ files

*.fastq.gz

cmo_options

:map

Optional Cell Ranger CMO section options as a Map. Supported keys: min-assignment-confidence.

meta7

:map

Groovy Map containing sample information

crispr_fastqs

:file

FASTQ files

*.fastq.gz

crispr_options

:map

Optional Cell Ranger feature section options for CRISPR Guide Capture as a Map. Pass null to disable this modality. Supported keys: r1-length, r2-length.

meta8

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

gex_reference

:directory

Folder containing Cellranger gene expression reference. Also required for feature barcode libraries without GEX FASTQs.

meta9

:map

Groovy Map containing sample information

vdj_t_fastqs

:file

T cell receptor (alpha/beta) V(D)J FASTQ files (feature type VDJ-T)

*.fastq.gz

vdj_t_options

:map

Optional Cell Ranger VDJ section options as a Map. See vdj_options.

meta10

:map

Groovy Map containing sample information

vdj_t_gd_fastqs

:file

T cell receptor (gamma/delta) V(D)J FASTQ files (feature type VDJ-T-GD). Cell Ranger requires custom inner enrichment primers (vdj_primer_index) for this library type.

*.fastq.gz

vdj_t_gd_options

:map

Optional Cell Ranger VDJ section options as a Map. See vdj_options.

meta11

:map

Groovy Map containing sample information

vdj_b_fastqs

:file

B cell receptor V(D)J FASTQ files (feature type VDJ-B)

*.fastq.gz

vdj_b_options

:map

Optional Cell Ranger VDJ section options as a Map. See vdj_options.

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

vdj_primer_index

:file

List of custom V(D)J inner enrichment primers; required for VDJ-T-GD libraries

*.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

ocm_barcodes

:file

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

*.csv

skip_renaming

:boolean

Skip renaming

Output

name:type
description
pattern

config

meta

:map

Groovy Map containing sample information

cellranger_multi_config.csv

:file

The resolved Cellranger multi config used for analysis

cellranger_multi_config.csv

outs

meta

:map

Groovy Map containing sample information

**/outs/**

:file

Files containing the outputs of Cell Ranger

${meta.id}/outs/*

versions_cellranger

${task.process}

:string

The name of the process

cellranger

:string

The name of the tool

cellranger --version | sed "s/.* //"

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

cellranger

:string

The name of the tool

cellranger --version | sed "s/.* //"

:eval

The expression to obtain the version of the tool

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
included in
scrnaseq
maintainer
Github user klkeys
get in touch
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