Description

Module to use Cell Ranger’s pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz

reference (directory)

Folder containing all the reference indices needed by Cell Ranger

Output

Name (Type)
Description
Pattern

outs (file)

Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list

${meta.id}/outs/*

versions (file)

File containing software version

versions.yml

Tools

cellranger
10x Genomics EULA

Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser.