Description

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

Input

name:type
description
pattern

meta

:map

Groovy Map containing genome information e.g. [ id:'genome' ]

fasta

:file

Reference genome FASTA file

*.{fasta,fa}

gtf

:file

Reference transcriptome GTF file

*.gtf

motifs

:file

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

*.txt

reference_config

:file

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

config

Output

name:type
description
pattern

reference

meta

:map

Groovy Map containing genome information e.g. [ id:'genome' ]

${prefix}

:directory

Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc

config

meta

:map

Groovy Map containing genome information e.g. [ id:'genome' ]

config

:file

Configuration file

versions_cellrangerarc

${task.process}

:string

The name of the process

cellrangerarc

:string

The name of the tool

cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

cellrangerarc

:string

The name of the tool

cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'

:eval

The expression to obtain the version of the tool

Tools

cellrangerarc
10x Genomics EULA

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

support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
included in
scrnaseq
maintainers
Github user ggabernet
Github user heylf
get in touch
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