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

meta:file

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

${meta.id}/outs/*

**/outs/**:file

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

${meta.id}/outs/*

versions

versions.yml: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.

support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj
airrflow
Github user ggabernet
Github user edmundmiller
Github user klkeys
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