Nextflow Registry | nf-core/soupx@0.0.0-e012934

nf-core/soupx @ 0.0.0-e012934

Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.

The filtered counts are preprocessed with Seurat (LogNormalize, PCA, kNN graph, clustering) to provide cluster assignments to SoupX, which then estimates per-cluster contamination and adjusts counts. The adjusted counts are written to the output H5AD as an ambient layer.

single-cell transcriptomics ambient

Latest version: 0.0.0-e012934

Total downloads: 0

Source: nf-core/modules

Authors: @LeonHafner

Maintainers: @LeonHafner @nictru

Summary

Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.

Get started

Add the following snippet to your workflow script to include this module.

include { SOUPX } from 'nf-core/soupx'

License

MIT License

Process

`Name`	`SOUPX`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`h5ad_filtered` file	filtered H5AD file (after CellRanger filtering) `*.h5ad`
`h5ad_raw` file	raw H5AD file (before CellRanger filtering) `*.h5ad`

`npcs` integer	Number of principal components for Seurat PCA (also controls FindNeighbors dims = 1:npcs).

`cluster_algorithm` integer	Seurat FindClusters algorithm identifier passed to `FindClusters(algorithm = ...)`. Valid values: 1: louvain 2: louvain_multilevel 3: slm 4: leiden

Output 2 channels

#1 h5ad tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.h5ad` file	H5AD anndata object with ambient RNA removed `*.h5ad`

#2 versions_soupx

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
soupx	Estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data	n/a

Version	0.0.0-e012934
Commit ID	e01293407a5949a1ffc9f007d6c1c2b520ea685a
Release Date	25 May 2026 15:00:55 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsoupx/0.0.0-e012934/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/soupx/blobs/sha256:e206e15ef6ea205017dae5c324eb4acd009a7da92b6855d65f3e422f3e83992e
Size	3.8 KB
Checksum	sha256:e206e15ef6ea205017dae5c324eb4acd009a7da92b6855d65f3e422f3e83992e
Downloads	0

Version	Date	Status	Downloads	Size	Diff
0.0.0-e012934	25 May 2026 15:00:55 (UTC)		0	3.8 KB	-