nf-core/cellrangeratac/count @ 0.0.0-0c7146d
Summary
Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC.
Get started
Add the following snippet to your workflow script to include this module.
include { CELLRANGERATAC_COUNT } from 'nf-core/cellrangeratac/count'
License
MIT License
Process
Name
|
CELLRANGERATAC_COUNT |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reads
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively, plus an additional FastQ for the barcodes |
reference
directory
|
Directory containing all the reference indices needed by Cell Ranger ATAC |
|---|
Output
2 channels
#1
outs
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
${meta.id}/outs/*
file
|
Files containing the outputs of Cell Ranger ATAC sample-${meta.gem}/outs/*
|
#2
versions_cellrangeratac
tuple
${task.process}
string
|
The name of the process |
|---|---|
cellrangeratac
string
|
The name of the tool |
cellranger-atac --version | sed 's/.*cellranger-atac-//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| cellranger-atac | Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. | https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 3fc6d40d163d89ae44d40a00b9017d5a9df5170e |
| Release Date | 08 Apr 2026 18:51:08 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellrangeratac%2Fcount/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cellrangeratac/count/blobs/sha256:7475cae2cf3f6a95c76d792442f998a3d9093610a2889c3fb96e13cd752a40a9 |
| Size | 3.5 KB |
| Checksum | sha256:7475cae2cf3f6a95c76d792442f998a3d9093610a2889c3fb96e13cd752a40a9 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-3fc6d40 | 22 Apr 2026 15:05:35 (UTC) | 4 | 3.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:51:08 (UTC) | 3 | 3.5 KB |