Nextflow Registry | nf-core/scvitools/scar@0.0.0-0c7146d

nf-core/scvitools/scar @ 0.0.0-0c7146d

Module to use scAR to remove ambient RNA from single-cell RNA-seq data

single-cell scRNA-seq ambient RNA removal

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @nictru

Maintainers: @nictru

Module to use scAR to remove ambient RNA from single-cell RNA-seq data

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

include { SCVITOOLS_SCAR } from 'nf-core/scvitools/scar'

MIT License

Process

`Name`	`SCVITOOLS_SCAR`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`filtered` file	AnnData file containing filtered data (without empty droplets) `*.h5ad`
`unfiltered` file	AnnData file containing unfiltered data (with empty droplets) `*.h5ad`

`input_layer` string	Layer to use as input. Defaults to `X`.

`output_layer` string	Layer to save the denoised counts to. Defaults to `scar`.

`max_epochs` integer	Maximum number of epochs to train the model. Defaults to the heuristic default.

`n_batch` integer	Number of batches to use for generating the ambient profile. Defaults to 1. This can be increased to prevent out-of-memory errors.

Output 2 channels

#1 h5ad tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`*.h5ad` file	AnnData file containing decontaminated counts as `adata.X` `*.h5ad`

#2 versions

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

Tool	Description	Homepage
scvitools	scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data	n/a
scar	scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics.	n/a

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:35:23 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fscvitools%2Fscar/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/scvitools/scar/blobs/sha256:f0a8116b7b59df8a0d4b36f4c6bbec3c51c98eeff87e6ff766d1cc484ef5ce92
Size	3.5 KB
Checksum	sha256:f0a8116b7b59df8a0d4b36f4c6bbec3c51c98eeff87e6ff766d1cc484ef5ce92
Downloads	2

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:43:42 (UTC)		3	3.6 KB
0.0.0-0c7146d	08 Apr 2026 19:35:23 (UTC)		2	3.5 KB