Nextflow Registry | nf-core/gmmdemux@0.0.0-0b45cc0

nf-core/gmmdemux @ 0.0.0-0b45cc0

GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).

demultiplexing hashing-based deconvolution single-cell

Latest version: 0.0.0-0b45cc0

Total downloads: 1

Source: nf-core/modules

Authors: @mari-ga @maxozo @wxicu @Zethson

Maintainers: @mari-ga @maxozo @wxicu @Zethson

GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).

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

include { GMMDEMUX } from 'nf-core/gmmdemux'

MIT License

Process

`Name`	`GMMDEMUX`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`hto_matrix` file	path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters
`hto_names` string	Comma separated list of HTO names, without whitespace

`type_report` boolean	If true, full classification report is generated, otherwise the simplified classification report.

`summary_report` boolean	If true, summary report is generated.

`skip` file	Load a full classification report and skip the mtx folder as input. Require a path argument.

`examine` file	Provide the cell list. Requires a file argument. Only executes if -u is set.

Output 7 channels

#1 matrix tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`matrix.mtx.gz` file	matrix mtx.tsv file with removed cell-hashing-identifiable multiplets `matrix.mtx.gz`

#2 barcodes tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`barcodes.tsv.gz` file	barcodes tsv file with removed cell-hashing-identifiable multiplets `barcodes.tsv.gz`

#3 features tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`features.tsv.gz` file	features tsv file with removed cell-hashing-identifiable multiplets `features.tsv.gz`

#4 config_report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`GMM_*.config` file	Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report. `GMM_*.csv`

#5 summary_report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`summary_report_*.txt` file	summary report, optional output `test/summary_report_*.txt`

#6 versions_gmmdemux tuple

`${task.process}` string	The name of the process
`GMM-Demux` string	The name of the tool
`0.2.2.3` string	The expression to obtain the version of the tool

#7 classification_report tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`GMM_*.csv` file	full or simplified classification report `GMM_*.csv`

Tool	Description	Homepage
gmmdemux	GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq).	https://pypi.org/project/GMM-Demux/

Version	0.0.0-0b45cc0
Commit ID	0b45cc097cafcd4768e2f79b504333fee85940bc