modules/cellrangerarc_mkgtf

Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command.

referencemkrefindex

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

Description

Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command.

Input

Name (Type)

Description

Pattern

`gtf` (file)

The reference GTF transcriptome file

*.gtf

Output

Name (Type)

Description

Pattern

`gtf` (directory)

The filtered GTF transcriptome file

*.filtered.gtf

`versions` (file)

File containing software version

versions.yml

Tools

cellrangerarc
10x Genomics EULA

Cell Ranger Arc 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-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

modules/cellrangerarc_mkgtf

Description