nf-core/cellrangeratac/mkref @ 0.0.0-0c7146d
Summary
Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command.
Get started
Add the following snippet to your workflow script to include this module.
include { CELLRANGERATAC_MKREF } from 'nf-core/cellrangeratac/mkref'
License
MIT License
Process
Name
|
CELLRANGERATAC_MKREF |
|---|
Input
5 channels
fasta
file
|
Reference genome FASTA file *.{fasta,fa}
|
|---|
gtf
file
|
Reference transcriptome GTF file *.gtf
|
|---|
motifs
file
|
Sequence motif file (e.g., of transcription factors) *.txt
|
|---|
reference_config
file
|
JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path config
|
|---|
reference_name
string
|
The name to give the new reference folder str
|
|---|
Output
2 channels
#1
reference
${reference_name}
directory
|
Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC |
|---|
#2
versions_cellrangeratac
tuple
${task.process}
string
|
The name of the process |
|---|---|
cellrangeratac
string
|
The name of the tool |
cellranger-atac --version 2>&1 | 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 | 4e8e48c04e24c2159a5589a36bae0f038809cd48 |
| Release Date | 08 Apr 2026 18:30:08 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcellrangeratac%2Fmkref/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cellrangeratac/mkref/blobs/sha256:7d2ecb073b50feff3a868bd21d161ae764781492bf5445620fd97186060df34d |
| Size | 2.8 KB |
| Checksum | sha256:7d2ecb073b50feff3a868bd21d161ae764781492bf5445620fd97186060df34d |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:30:08 (UTC) | 1 | 2.8 KB | - |