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

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.