nf-core/demuxem @ 0.0.0-3fc6d40
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:10:15 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fdemuxem/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/demuxem/blobs/sha256:bdc4e29d693d37908ee331338a8dcbc8f6e29659574033d00bb39f44c2c8f181 |
| Size | 3.2 KB |
| Checksum | sha256:bdc4e29d693d37908ee331338a8dcbc8f6e29659574033d00bb39f44c2c8f181 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:14:03 (UTC) | 3 | 3.2 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:10:15 (UTC) | 3 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:57:27 (UTC) | 3 | 3.2 KB |