Description

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

Input

name:type
description
pattern

bcl{:bash}

:file

Base call files

*.bcl.bgzf

csv{:bash}

:file

Sample sheet

*.csv

Output

name:type
description
pattern

fastq{:bash}

${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz{:bash}

:file

Unaligned FastQ files

*.fastq.gz

versions_cellrangeratac{:bash}

${task.process}{:bash}

:string

The name of the process

cellrangeratac{:bash}

:string

The name of the tool

cellranger-atac --version | sed 's/.*cellranger-atac-//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

cellrangeratac{:bash}

:string

The name of the tool

cellranger-atac --version | sed 's/.*cellranger-atac-//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

cellranger-atac
10x Genomics EULA

Cell Ranger ATAC 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-atac/software/pipelines/latest/what-is-cell-ranger-atac
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