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{:bash}`
`:file`

The reference GTF transcriptome file

*.gtf

Output

name:type

description

pattern

`gtf{:bash}`

`*.gtf{:bash}`
`:directory`

The filtered GTF transcriptome file

*.filtered.gtf

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software version

versions.yml

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{:bash}`
`:file`

Output

`gtf{:bash}`

`*.gtf{:bash}`
`:directory`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

cellranger
10X Genomics EULA

included in

maintainers

get in touch

modules/cellranger_mkgtf

Description

Input

gtf{:bash}:file

Output

gtf{:bash}

*.gtf{:bash}:directory

versions{:bash}

versions.yml{:bash}:file

Tools

cellranger 10X Genomics EULA

included in

maintainers

get in touch

`gtf{:bash}`
`:file`

`gtf{:bash}`

`*.gtf{:bash}`
`:directory`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

cellranger
10X Genomics EULA