modules/gmmdemux

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

demultiplexinghashing-based deconvolutionsingle-cell

https://github.com/nf-core/modules/[...]/modules/nf-core/gmmdemux

Description

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

Input

name:type

description

pattern

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1']

`hto_matrix{:bash}`
`:file`

path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters

`hto_names{:bash}`
`:string`

Comma separated list of HTO names, without whitespace

`type_report{:bash}`
`:boolean`

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

`summary_report{:bash}`
`:boolean`

If true, summary report is generated.

`skip{:bash}`
`:file`

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

`examine{:bash}`
`:file`

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

Output

name:type

description

pattern

`barcodes{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`barcodes.tsv.gz{:bash}`
`:file`

barcodes tsv file with removed cell-hashing-identifiable multiplets

barcodes.tsv.gz

`matrix{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`matrix.mtx.gz{:bash}`
`:file`

matrix mtx.tsv file with removed cell-hashing-identifiable multiplets

matrix.mtx.gz

`features{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`features.tsv.gz{:bash}`
`:file`

features tsv file with removed cell-hashing-identifiable multiplets

features.tsv.gz

`classification_report{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`GMM_*.csv{:bash}`
`:file`

full or simplified classification report

GMM_*.csv

`config_report{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`GMM_*.config{:bash}`
`:file`

Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report.

GMM_*.csv

`summary_report{:bash}`

`meta{:bash}`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`summary_report_*.txt{:bash}`
`:file`

summary report, optional output

test/summary_report_*.txt

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

gmmdemux
MIT

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

pypi.org/project/GMM-Demux github.com/CHPGenetics/GMM-Demux https://github.com/CHPGenetics/GMM-demux 10.1186/s13059-020-02084-2