Description

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

Input

name:type
description
pattern

fasta{:bash}

:file

Reference genome FASTA file

*.{fasta,fa}

gtf{:bash}

:file

Reference transcriptome GTF file

*.gtf

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 containing all the reference indices needed by Cell Ranger

versions_cellranger{:bash}

${task.process}{:bash}

:string

The name of the process

cellranger{:bash}

:string

The name of the tool

cellranger --version | sed "s/.*-//"{: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

cellranger{:bash}

:string

The name of the tool

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

:eval

The expression to obtain the version of the tool

Tools

cellranger
10X Genomics EULA

Cell Ranger 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-gene-expression/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
included in
scrnaseq
maintainer
Github user ggabernet
get in touch
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