modules/cellranger_mkgtf

Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.

referencemkrefindex

https://github.com/nf-core/modules/[...]/modules/nf-core/cellranger/mkgtf

Description

Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command.

Input

name:type

description

pattern

`gtf`
`:file`

The reference GTF transcriptome file

*.gtf

Output

name:type

description

pattern

`gtf`

`*.gtf`
`:directory`

The filtered GTF transcriptome file

*.filtered.gtf

`versions_cellranger`

`${task.process}`
`:string`

The name of the process

`cellranger`
`:string`

The name of the tool

`cellranger --version | sed "s/.*-//"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`cellranger`
`:string`

The name of the tool

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

modules/cellranger_mkgtf

Description

Input

`gtf`
`:file`

Output

`gtf`

`*.gtf`
`:directory`

`versions_cellranger`

`${task.process}`
`:string`

`cellranger`
`:string`

`cellranger --version | sed "s/.*-//"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`cellranger`
`:string`

`cellranger --version | sed "s/.*-//"`
`:eval`

Tools

cellranger
10X Genomics EULA

included in

maintainers

get in touch

modules/cellranger_mkgtf

Description

Input

gtf:file

Output

gtf

*.gtf:directory

versions_cellranger

${task.process}:string

cellranger:string

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

Topics

versions

${task.process}:string

cellranger:string

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

Tools

cellranger 10X Genomics EULA

included in

maintainers

get in touch

`gtf`
`:file`

`gtf`

`*.gtf`
`:directory`

`versions_cellranger`

`${task.process}`
`:string`

`cellranger`
`:string`

`cellranger --version | sed "s/.*-//"`
`:eval`

`versions`

`${task.process}`
`:string`

`cellranger`
`:string`

`cellranger --version | sed "s/.*-//"`
`:eval`

cellranger
10X Genomics EULA