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

${reference_name}

:directory

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

versions_cellrangeratac

${task.process}

:string

The name of the process

cellrangeratac

:string

The name of the tool

cellranger-atac --version 2>&1 | sed 's/.*cellranger-atac-//'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

cellrangeratac

:string

The name of the tool

cellranger-atac --version 2>&1 | sed 's/.*cellranger-atac-//'

:eval

The expression to obtain the version of the tool

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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