Nextflow Registry | nf-core/scanpy/hashsolo@0.0.0-0c7146d

nf-core/scanpy/hashsolo @ 0.0.0-0c7146d

Probabilistic demultiplexing of cell hashing data

anndata single-cell hashing demultiplexing scanpy

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @seohyonkim @LuisHeinzlmeier

Maintainers: @seohyonkim @LuisHeinzlmeier

Probabilistic demultiplexing of cell hashing data

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

include { SCANPY_HASHSOLO } from 'nf-core/scanpy/hashsolo'

MIT License

Process

`Name`	`SCANPY_HASHSOLO`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`data` file	A directory in 10x Genomics format containing `matrix.mtx.gz`, `features.tsv.gz`, `barcodes.tsv.gz` (hashing count matrix), or an AnnData (`.h5ad`) file with hashing counts stored in `.obs`.
`cell_hashing_columns` list	Groovy list (`['hash_1', 'hash_2']`) of `.obs` columns that contain cell hashing counts. Can be `[]` if the data is in 10x Genomics format, as the columns are derived from the input.

Output 4 channels

#1 h5ad tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_hashsolo.h5ad` file	Processed AnnData object containing hashsolo results `*_hashsolo.h5ad`

#2 params tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]` `*_params_hashsolo.csv`
`*_params_hashsolo.csv` file	CSV file containing parameters used in hashsolo analysis `*_params_hashsolo.csv`

#3 versions

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

#4 assignment tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_assignment_hashsolo.csv` file	CSV file containing hashsolo assignment results `*_assignment_hashsolo.csv`

Tool	Description	Homepage
scanpy	Single-cell analysis in Python. Scales to >100M cells.	https://github.com/scverse/scanpy

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:34:24 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fscanpy%2Fhashsolo/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/scanpy/hashsolo/blobs/sha256:db21e5c88191861cfe113b7297e767e2466ba53f411661ff8427c5e01514b5e4
Size	6.4 KB
Checksum	sha256:db21e5c88191861cfe113b7297e767e2466ba53f411661ff8427c5e01514b5e4
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:43:34 (UTC)		3	6.5 KB
0.0.0-0c7146d	08 Apr 2026 19:34:24 (UTC)		4	6.4 KB