nf-core/spaceranger/count @ 0.0.0-3fc6d40
Summary
Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data
Get started
Add the following snippet to your workflow script to include this module.
include { SPACERANGER_COUNT } from 'nf-core/spaceranger/count'
License
MIT License
Name
|
SPACERANGER_COUNT |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', slide:'10L13-020', area: 'B1']
|
|---|---|
reads
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. ${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz
|
image
file
|
Brightfield tissue H&E image in JPEG or TIFF format. *.{tif,tiff,jpg,jpeg}
|
slide
string
|
Visium slide ID used for the sample. |
area
string
|
Visium slide capture area used for the sample. |
cytaimage
file
|
CytAssist instrument captured eosin stained Brightfield tissue image with fiducial frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should not be modified any way before passing it as input to either Space Ranger or Loupe Browser. *.{tif,tiff}
|
darkimage
file
|
Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files. *.{tif,tiff,jpg,jpeg}
|
colorizedimage
file
|
Required for color composite fluorescence microscope image input. A color composite of one or more fluorescence image channels saved as a single-page, single-file color TIFF or JPEG. *.{tif,tiff,jpg,jpeg}
|
alignment
file
|
OPTIONAL - Path to manual image alignment. *.json
|
slidefile
file
|
OPTIONAL - Path to slide specifications. *.json
|
reference
directory
|
Folder containing all the reference indices needed by Space Ranger |
|---|
probeset
file
|
OPTIONAL - Probe set specification. *.csv
|
|---|
outs
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
outs/**
file
|
Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list outs/*
|
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 15:32:31 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fspaceranger%2Fcount/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/spaceranger/count/blobs/sha256:9939c2a582ba8c53ffe635066a26510b983adbfc77b08d15fb35668b14853894 |
| Size | 7.7 KB |
| Checksum | sha256:9939c2a582ba8c53ffe635066a26510b983adbfc77b08d15fb35668b14853894 |
| Downloads | 4 |