modules/deeptools_computematrix

calculates scores per genome regions for other deeptools plotting utilities

genomeregionsscoresmatrix

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

Description

calculates scores per genome regions for other deeptools plotting utilities

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`bigwig`
`:file`

bigwig file containing genomic scores

*.{bw,bigwig}

`bed`
`:file`

bed file containing genomic regions

*.{bed}

Output

name:type

description

pattern

`matrix`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.mat.gz`
`:file`

gzipped matrix file needed by the plotHeatmap and plotProfile deeptools utilities

*.{computeMatrix.mat.gz}

`table`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.mat.tab`
`:file`

tabular file containing the scores of the generated matrix

*.{computeMatrix.vals.mat.tab}

`versions_deeptools`

`${task.process}`
`:string`

The name of the process

`deeptools`
`:string`

The name of the tool

`computeMatrix --version | sed "s/computeMatrix //g"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`deeptools`
`:string`

The name of the tool

`computeMatrix --version | sed "s/computeMatrix //g"`
`:eval`

The expression to obtain the version of the tool

Tools

deeptools
GPL v3

A set of user-friendly tools for normalization and visualization of deep-sequencing data

deeptools.readthedocs.io/en/develop https://github.com/deeptools/deepTools 10.1093/nar/gku365

modules/deeptools_computematrix

Description

Input

`meta`
`:map`

`bigwig`
`:file`

`bed`
`:file`

Output

`matrix`

`meta`
`:map`

`*.mat.gz`
`:file`

`table`

`meta`
`:map`

`*.mat.tab`
`:file`

`versions_deeptools`

`${task.process}`
`:string`

`deeptools`
`:string`

`computeMatrix --version | sed "s/computeMatrix //g"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`deeptools`
`:string`

`computeMatrix --version | sed "s/computeMatrix //g"`
`:eval`

Tools

deeptools
GPL v3

included in

maintainers

get in touch

modules/deeptools_computematrix

Description

Input

meta:map

bigwig:file

bed:file

Output

matrix

meta:map

*.mat.gz:file

table

meta:map

*.mat.tab:file

versions_deeptools

${task.process}:string

deeptools:string

computeMatrix --version | sed "s/computeMatrix //g":eval

Topics

versions

${task.process}:string

deeptools:string

computeMatrix --version | sed "s/computeMatrix //g":eval

Tools

deeptools GPL v3

included in

maintainers

get in touch

`meta`
`:map`

`bigwig`
`:file`

`bed`
`:file`

`matrix`

`meta`
`:map`

`*.mat.gz`
`:file`

`table`

`meta`
`:map`

`*.mat.tab`
`:file`

`versions_deeptools`

`${task.process}`
`:string`

`deeptools`
`:string`

`computeMatrix --version | sed "s/computeMatrix //g"`
`:eval`

`versions`

`${task.process}`
`:string`

`deeptools`
`:string`

`computeMatrix --version | sed "s/computeMatrix //g"`
`:eval`

deeptools
GPL v3