modules/wisecondorx_predict

Find copy number aberrations

copy number variationbednpzpng

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

Description

Find copy number aberrations

Input

name:type

description

pattern

`meta`
`:map`

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

`npz`
`:file`

An NPZ file created with WisecondorX convert

*.npz

`meta2`
`:map`

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

`reference`
`:file`

A reference NPZ file created with WisecondorX newref

*.npz

`meta3`
`:map`

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

`blacklist`
`:file`

OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)

*.bed

Output

name:type

description

pattern

`aberrations_bed`

`meta`
`:map`

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

*_aberrations.bed

`*_aberrations.bed`
`:map`

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

*_aberrations.bed

`bins_bed`

`meta`
`:map`

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

*_aberrations.bed

`*_bins.bed`
`:map`

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

*_bins.bed

`segments_bed`

`meta`
`:map`

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

*_aberrations.bed

`*_segments.bed`
`:map`

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

*_segments.bed

`chr_statistics`

`meta`
`:map`

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

*_aberrations.bed

`*_statistics.txt`
`:map`

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

*_chr_statistics.txt

`chr_plots`

`meta`
`:map`

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

*_aberrations.bed

`[!genome_wide]*.png`
`:map`

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

[!genome_wide]*.png

`genome_plot`

`meta`
`:map`

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

*_aberrations.bed

`genome_wide.png`
`:map`

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

genome_wide.png

`versions_wisecondorx`

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

The name of the process

`wisecondorx`
`:string`

The name of the tool

`pip list |& sed -n 's/wisecondorx *//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`wisecondorx`
`:string`

The name of the tool

`pip list |& sed -n 's/wisecondorx *//p'`
`:eval`

The expression to obtain the version of the tool

Tools

wisecondorx
Attribution-NonCommercial-ShareAlike CC BY-NC-SA

WIthin-SamplE COpy Number aberration DetectOR, including sex chromosomes

github.com/CenterForMedicalGeneticsGhent/WisecondorX 10.1093/nar/gky1263

modules/wisecondorx_predict

Description

Input

meta:map

npz:file

meta2:map

reference:file

meta3:map

blacklist:file

Output

aberrations_bed

meta:map

*_aberrations.bed:map

bins_bed

meta:map

*_bins.bed:map

segments_bed

meta:map

*_segments.bed:map

chr_statistics

meta:map

*_statistics.txt:map

chr_plots

meta:map

[!genome_wide]*.png:map

genome_plot

meta:map

genome_wide.png:map

versions_wisecondorx

${task.process}:string

wisecondorx:string

pip list |& sed -n 's/wisecondorx *//p':eval

Topics

versions

${task.process}:string

wisecondorx:string

pip list |& sed -n 's/wisecondorx *//p':eval

Tools

wisecondorx Attribution-NonCommercial-ShareAlike CC BY-NC-SA

maintainer

get in touch

`meta`
`:map`

`npz`
`:file`

`meta2`
`:map`

`reference`
`:file`

`meta3`
`:map`

`blacklist`
`:file`

`aberrations_bed`

`meta`
`:map`

`*_aberrations.bed`
`:map`

`bins_bed`

`meta`
`:map`

`*_bins.bed`
`:map`

`segments_bed`

`meta`
`:map`

`*_segments.bed`
`:map`

`chr_statistics`

`meta`
`:map`

`*_statistics.txt`
`:map`

`chr_plots`

`meta`
`:map`

`[!genome_wide]*.png`
`:map`

`genome_plot`

`meta`
`:map`

`genome_wide.png`
`:map`

`versions_wisecondorx`

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

`wisecondorx`
`:string`

`pip list |& sed -n 's/wisecondorx *//p'`
`:eval`

`versions`

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

`wisecondorx`
`:string`

`pip list |& sed -n 's/wisecondorx *//p'`
`:eval`

wisecondorx
Attribution-NonCommercial-ShareAlike CC BY-NC-SA