nf-core/spaceranger/mkgtf @ 0.0.0-3fc6d40
Summary
Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command.
Get started
Add the following snippet to your workflow script to include this module.
include { SPACERANGER_MKGTF } from 'nf-core/spaceranger/mkgtf'
License
MIT License
Process
Name
|
SPACERANGER_MKGTF |
|---|
Input
1 channel
gtf
file
|
The reference GTF transcriptome file *.gtf
|
|---|
Output
2 channels
#1
gtf
*.gtf
directory
|
The filtered GTF transcriptome file *.filtered.gtf
|
|---|
#2
versions_spaceranger
tuple
${task.process}
string
|
The name of the process |
|---|---|
spaceranger
string
|
The name of the tool |
spaceranger -V | sed "s/spaceranger spaceranger-//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| spaceranger | Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows users to map the whole transcriptome in formalin fixed paraffin embedded (FFPE) and fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research. Space Ranger provides pipelines for end to end analysis of Visium Spatial Gene Expression experiments. | https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 3fc6d40d163d89ae44d40a00b9017d5a9df5170e |
| Release Date | 22 Apr 2026 15:32:32 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fspaceranger%2Fmkgtf/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/spaceranger/mkgtf/blobs/sha256:ca9b7afcc27354dc87df706d95a705afe48bbbac557a3dbf5f64fa4cd86afb2a |
| Size | 2.3 KB |
| Checksum | sha256:ca9b7afcc27354dc87df706d95a705afe48bbbac557a3dbf5f64fa4cd86afb2a |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-3fc6d40 | 22 Apr 2026 15:32:32 (UTC) | 3 | 2.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:40:01 (UTC) | 2 | 2.3 KB |