nf-core/xeniumranger/resegment @ 0.0.0-3fc6d40
Summary
The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters.
Get started
Add the following snippet to your workflow script to include this module.
include { XENIUMRANGER_RESEGMENT } from 'nf-core/xeniumranger/resegment'
License
MIT License
Process
Name
|
XENIUMRANGER_RESEGMENT |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing run information e.g. [ id:'xenium_experiment' ] |
|---|---|
xenium_bundle
directory
|
Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline |
Output
2 channels
#1
outs
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
${prefix}
directory
|
Directory containing the output xenium bundle of Xenium Ranger ${prefix}
|
#2
versions_xeniumranger
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
xeniumranger
string
|
The tool name |
xeniumranger -V | sed -e 's/.*xenium-//'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| xeniumranger | Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells. | https://www.10xgenomics.com/support/software/xenium-ranger/latest |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 3fc6d40d163d89ae44d40a00b9017d5a9df5170e |
| Release Date | 22 Apr 2026 15:37:05 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fxeniumranger%2Fresegment/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/xeniumranger/resegment/blobs/sha256:14a09333e16d1aa623ed7b0d1704ba9ce9ff0a055994761bf45842a52b92f4c1 |
| Size | 2.7 KB |
| Checksum | sha256:14a09333e16d1aa623ed7b0d1704ba9ce9ff0a055994761bf45842a52b92f4c1 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-3fc6d40 | 22 Apr 2026 15:37:05 (UTC) | 3 | 2.7 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:48:13 (UTC) | 4 | 2.6 KB |