Description

Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command.

Input

name:type
description
pattern

fasta:file

Reference genome FASTA file

*.{fasta,fa}

gtf:file

Reference transcriptome GTF file

*.gtf

motifs:file

Sequence motif file (e.g., of transcription factors)

*.txt

reference_config:file

JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path

config

reference_name:string

The name to give the new reference folder

str

Output

name:type
description
pattern

reference:directory

Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC

versions:file

File containing software version

versions.yml

Tools

cellranger-atac
10x Genomics EULA

Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.

support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac
maintainers
Github user ggabernet
Github user heylf
get in touch
Ask a question on Slack Open an issue on GitHub