nf-core/cellrangerarc/count @ 0.0.0-5d5b444
Summary
Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command.
Get started
Add the following snippet to your workflow script to include this module.
include { CELLRANGERARC_COUNT } from 'nf-core/cellrangerarc/count'
License
MIT License
Name
|
CELLRANGERARC_COUNT |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
sample_type
string
|
The type of sample |
sub_sample
string
|
The name of sub sample |
reads
file
|
FASTQ files produced using Cell Ranger ARC *.fastq.gz
|
meta2
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
reference
directory
|
Directory containing all the reference indices needed by Cell Ranger ARC |
lib
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
${prefix}_lib.csv
file
|
Library ${prefix}_lib.csv
|
outs
tuple
meta
map
|
Groovy Map containing sample information |
|---|---|
${prefix}/outs/**
file
|
Files containing the outputs of Cell Ranger ARC ${prefix}/outs/*
|
versions_cellrangerarc
tuple
${task.process}
string
|
The name of the process |
|---|---|
cellrangerarc
string
|
The name of the tool |
cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| cellrangerarc | Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data. | https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc |
| Version | 0.0.0-5d5b444 |
|---|---|
| Commit ID | 3fc6d40d163d89ae44d40a00b9017d5a9df5170e |
| Release Date | 21 Apr 2026 15:00:41 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellrangerarc%2Fcount/0.0.0-5d5b444/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/cellrangerarc/count/blobs/sha256:99bda99655f1ef22af3c504a4d8f102623b365a5454134990df492725ef57a27 |
| Size | 5.5 KB |
| Checksum | sha256:99bda99655f1ef22af3c504a4d8f102623b365a5454134990df492725ef57a27 |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-3fc6d40 | 22 Apr 2026 15:05:30 (UTC) | 3 | 5.6 KB | |
| 0.0.0-5d5b444 | 21 Apr 2026 15:00:41 (UTC) | 4 | 5.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:51:00 (UTC) | 3 | 5.5 KB |