Nextflow Registry | nf-core/hasheddrops@0.0.0-6c4ed3a

nf-core/hasheddrops @ 0.0.0-6c4ed3a

Generating cell hashing calls from a matrix of count data.

demultiplexing hashing-based deconvolution single-cell

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @LuisHeinzlmeier

Maintainers: @LuisHeinzlmeier

Generating cell hashing calls from a matrix of count data.

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

include { HASHEDDROPS } from 'nf-core/hasheddrops'

MIT License

Process

`Name`	`HASHEDDROPS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`hto_matrix` file	Directory that contains the HTO matrix in a 10X format.
`runEmptyDrops` boolean	Run EmptyDrops() before hashedDrops() ("TRUE") or not ("FALSE").
`rna_matrix` file	Path to RNA count matrix, which is only uses if runEmptyDrops == "TRUE".

Output 9 channels

#1 rds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_hasheddrops.rds` file	HashedDrops results in RDS format `_hasheddrops.rds`

#2 plot tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_plot_hasheddrops.png` file	HashedDrops plot `_plot_hasheddrops.png`

#3 params tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_params_hasheddrops.csv` file	The used parameters to call hashedDrops() in the R-Script. `_params_hasheddrops.csv`

#4 results tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_results_hasheddrops.csv` file	HashedDrops results `_results_hasheddrops.csv`

#5 versions

`versions.yml` file	File containing software versions.

#6 id_to_hash tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_id_to_hash.csv` file	A table mapping integer indices used by hashedDrops results (e.g. the column `Best` or `Second`) to HTO names (or combinations of HTO names joined with `+` if `combinations` is speficied in `ext.args`). `_id_to_hash.csv`

#7 empty_drops_csv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_emptyDrops.csv` file	EmptyDrops results in CSV format `_emptyDrops.csv`

#8 empty_drops_rds tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_emptyDrops.rds` file	EmptyDrops results in RDS format `_emptyDrops.rds`

#9 empty_drops_plot tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*_emptyDrops.png` file	EmptyDrops results plot `_emptyDrops.png`

Tool	Description	Homepage
hasheddrops	Demultiplex cell barcodes into their samples of origin based on the most abundant hash tag oligo (HTO). Also identify potential doublets based on the presence of multiple significant HTOs.	https://rdrr.io/github/MarioniLab/DropletUtils/man/hashedDrops.html

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:23:39 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-