modules/controlfreec_makegraph2

Plot Freec output

cnacnvsomaticsingletumor-only

https://github.com/nf-core/modules/[...]/modules/nf-core/controlfreec/makegraph2

Description

Plot Freec output

Input

name:type

description

pattern

`meta`
`:map`

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

`ratio`
`:file`

ratio file generated by FREEC

*.ratio.txt

`baf`
`:file`

.BAF file generated by FREEC

*.BAF

Output

name:type

description

pattern

`png_baf`

`meta`
`:map`

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

`*_BAF.png`
`:file`

Image of BAF plot

*_BAF.png

`png_ratio_log2`

`meta`
`:map`

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

`*_ratio.log2.png`
`:file`

Image of ratio log2 plot

*_ratio.log2.png

`png_ratio`

`meta`
`:map`

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

`*_ratio.png`
`:file`

Image of ratio plot

*_ratio.png

`versions_controlfreec`

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

The name of the process

`controlfreec`
`:string`

The name of the tool

`11.6b`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`controlfreec`
`:string`

The name of the tool

`11.6b`
`:string`

The expression to obtain the version of the tool

Tools

controlfreec
GPL >=2

Copy number and genotype annotation from whole genome and whole exome sequencing data.

http://boevalab.inf.ethz.ch/FREEC http://boevalab.inf.ethz.ch/FREEC/tutorial https://github.com/BoevaLab/FREEC/ 10.1093/bioinformatics/btq635

modules/controlfreec_makegraph2

Description

Input

`meta`
`:map`

`ratio`
`:file`

`baf`
`:file`

Output

`png_baf`

`meta`
`:map`

`*_BAF.png`
`:file`

`png_ratio_log2`

`meta`
`:map`

`*_ratio.log2.png`
`:file`

`png_ratio`

`meta`
`:map`

`*_ratio.png`
`:file`

`versions_controlfreec`

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

`controlfreec`
`:string`

`11.6b`
`:string`

Topics

`versions`

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

`controlfreec`
`:string`

`11.6b`
`:string`

Tools

controlfreec
GPL >=2

included in

maintainer

get in touch

modules/controlfreec_makegraph2

Description

Input

meta:map

ratio:file

baf:file

Output

png_baf

meta:map

*_BAF.png:file

png_ratio_log2

meta:map

*_ratio.log2.png:file

png_ratio

meta:map

*_ratio.png:file

versions_controlfreec

${task.process}:string

controlfreec:string

11.6b:string

Topics

versions

${task.process}:string

controlfreec:string

11.6b:string

Tools

controlfreec GPL >=2

included in

maintainer

get in touch

`meta`
`:map`

`ratio`
`:file`

`baf`
`:file`

`png_baf`

`meta`
`:map`

`*_BAF.png`
`:file`

`png_ratio_log2`

`meta`
`:map`

`*_ratio.log2.png`
`:file`

`png_ratio`

`meta`
`:map`

`*_ratio.png`
`:file`

`versions_controlfreec`

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

`controlfreec`
`:string`

`11.6b`
`:string`

`versions`

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

`controlfreec`
`:string`

`11.6b`
`:string`

controlfreec
GPL >=2