modules/deeptools_plotpca

Generates principal component analysis (PCA) plot using a compressed matrix generated by multibamsummary or multibigwigsummary as input.

PCAmatrixbambigwig

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

Description

Generates principal component analysis (PCA) plot using a compressed matrix generated by multibamsummary or multibigwigsummary as input.

Input

name:type

description

pattern

`meta`
`:map`

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

`matrix`
`:file`

compressed matrix file produced by mutlibamsummary or multibigwigsummary

*.{npz}

Output

name:type

description

pattern

`pdf`

`meta`
`:map`

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

`*.pdf`
`:file`

Output figure containing resulting plot

*.{plotPCA.pdf}

`tab`

`meta`
`:map`

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

`*.tab`
`:file`

Tab file containing data used to generate the PCA plot

*.{plotPCA.tab}

`versions_deeptools`

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

The name of the process

`deeptools`
`:string`

The name of the tool

`plotPCA --version | sed "s/plotPCA //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

`plotPCA --version | sed "s/plotPCA //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_plotpca

Description

Input

`meta`
`:map`

`matrix`
`:file`

Output

`pdf`

`meta`
`:map`

`*.pdf`
`:file`

`tab`

`meta`
`:map`

`*.tab`
`:file`

`versions_deeptools`

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

`deeptools`
`:string`

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

Topics

`versions`

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

`deeptools`
`:string`

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

Tools

deeptools
GPL v3

included in

maintainers

get in touch

modules/deeptools_plotpca

Description

Input

meta:map

matrix:file

Output

pdf

meta:map

*.pdf:file

tab

meta:map

*.tab:file

versions_deeptools

${task.process}:string

deeptools:string

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

Topics

versions

${task.process}:string

deeptools:string

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

Tools

deeptools GPL v3

included in

maintainers

get in touch

`meta`
`:map`

`matrix`
`:file`

`pdf`

`meta`
`:map`

`*.pdf`
`:file`

`tab`

`meta`
`:map`

`*.tab`
`:file`

`versions_deeptools`

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

`deeptools`
`:string`

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

`versions`

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

`deeptools`
`:string`

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

deeptools
GPL v3