Description

Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command.

Input

name:type
description
pattern

bcl:file

Base call files

*.bcl.bgzf

csv:file

Sample sheet

*.csv

Output

name:type
description
pattern

versions

versions.yml:file

File containing software version

versions.yml

fastq

${bcl.getSimpleName(:file

Unaligned FastQ files

*.fastq.gz

/*.fastq.gz:file

Unaligned FastQ files

*.fastq.gz

Tools

cellrangerarc
10x Genomics EULA

Cell Ranger Arc 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-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
maintainers
Github user ggabernet
Github user edmundmiller
Github user RHReynolds
Github user heylf
get in touch
Ask a question on Slack Open an issue on GitHub