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{:bash}

:file

Reference genome FASTA file

*.{fasta,fa}

gtf{:bash}

:file

Reference transcriptome GTF file

*.gtf

motifs{:bash}

:file

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

*.txt

reference_config{:bash}

: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{:bash}

:string

The name to give the new reference folder

str

Output

name:type
description
pattern

reference{:bash}

${reference_name}{:bash}

:directory

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

versions{:bash}

versions.yml{:bash}

: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
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