modules/cellranger_multi

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.

alignreferencecellrangermultiomicsgene expressionvdjantigen captureantibody capturecrispr

https://github.com/nf-core/modules/[...]/modules/nf-core/cellranger/multi

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

]

`meta_gex:map`

Groovy Map containing sample information

`gex_fastqs :file`

FASTQ files

*.fastq.gz

`meta_vdj:map`

Groovy Map containing sample information

`vdj_fastqs :file`

FASTQ files

*.fastq.gz

`meta_ab:map`

Groovy Map containing sample information

`ab_fastqs :file`

FASTQ files

*.fastq.gz

`meta_beam:map`

Groovy Map containing sample information

`beam_fastqs :file`

FASTQ files

*.fastq.gz

`meta_cmo:map`

Groovy Map containing sample information

`cmo_fastqs :file`

FASTQ files

*.fastq.gz

`meta_crispr:map`

Groovy Map containing sample information

`crispr_fastqs:file`

FASTQ files

*.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

`skip_renaming:boolean`

Skip renaming

Output

name:type

description

pattern

`config`

`meta:file`

The resolved Cellranger multi config used for analysis

cellranger_multi_config.csv

`cellranger_multi_config.csv:file`

The resolved Cellranger multi config used for analysis

cellranger_multi_config.csv

`outs`

`meta:file`

Files containing the outputs of Cell Ranger

${meta.id}/outs/*

`/outs/:file`

Files containing the outputs of Cell Ranger

${meta.id}/outs/*

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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