Description

Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.

Input

Name (Type)
Description
Pattern

bcl (file)

Base call files

*.bcl.bgzf

csv (file)

Sample sheet

*.csv

Output

Name (Type)
Description
Pattern

fastq (file)

Unaligned FastQ files

*.fastq.gz

versions (file)

File containing software version

versions.yml
authors
Github user ggabernet Github user Emiller88 Github user RHReynolds
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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_ov