nf-core/demuxem @ 0.0.0-0c7146d
Summary
Demultiplexing cell nucleus hashing data, using the estimated antibody background probability.
Get started
Add the following snippet to your workflow script to include this module.
include { DEMUXEM } from 'nf-core/demuxem'
License
MIT License
Name
|
DEMUXEM |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
input_raw_gene_bc_matrices_h5
string
|
Path to file containing input raw RNA expression matrix in 10x hdf5 format pattern: "*.{h5}" |
input_hto_csv_file
string
|
Path to file containing input HTO (antibody tag) count matrix in CSV format. *.{csv}
|
generate_gender_plot
string
|
Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names. |
|---|
genome
string
|
Reference genome name. If not provided, the tools infers it from the expression matrix file |
|---|
generate_diagnostic_plots
string
|
Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions. |
|---|
zarr
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample1' ] |
|---|---|
*_demux.zarr.zip
file
|
RNA expression matrix with demultiplexed sample identities in Zarr format. *_demux.zarr.zip
|
out_zarr
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'sample1' ] |
|---|---|
*.out.demuxEM.zarr.zip
file
|
DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA. *.out.demuxEM.zarr.zip
|
versions_demuxem
tuple
${task.process}
string
|
The name of the process |
|---|---|
demuxEM
string
|
The name of the tool |
demuxEM --version
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| demuxem | DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data. | https://demuxEM.readthedocs.io |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:35:56 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fdemuxem/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/demuxem/blobs/sha256:2119eb0cd4f41be056c67074820b568b390e35d02db9777b6b6d35b077f39ba6 |
| Size | 3.2 KB |
| Checksum | sha256:2119eb0cd4f41be056c67074820b568b390e35d02db9777b6b6d35b077f39ba6 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:35:56 (UTC) | 1 | 3.2 KB | - |