modules/cellranger_mkref

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

referencemkrefindex

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

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:file`

Reference genome FASTA file

*.{fasta,fa}

`gtf:file`

Reference transcriptome GTF file

*.gtf

`reference_name:string`

The name to give the new reference folder

str

Output

name:type

description

pattern

`reference`

`${reference_name}:directory`

Folder containing all the reference indices needed by Cell Ranger

`versions`

`versions.yml: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_mkref

Description

Input

fasta:file

gtf:file

reference_name:string

Output

reference

${reference_name}:directory

versions

versions.yml:file