modules/hmmcopy_mapcounter

mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file

hmmcopymapcountercnv

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

Description

mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file

Input

name:type

description

pattern

`meta`
`:map`

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

`bigwig`
`:file`

BigWig file with the mappability score of the genome, for instance made with generateMap function.

*.wig

Output

name:type

description

pattern

`wig`

`meta`
`:map`

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

`*.wig`
`:file`

wig file containing mappability of each window of the genome

*.wig

`versions_hmmcopy`

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

The name of the process

`hmmcopy`
`:string`

The name of the tool

`0.1.1`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`hmmcopy`
`:string`

The name of the tool

`0.1.1`
`:string`

The expression to obtain the version of the tool

Tools

hmmcopy
GPL v3

C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy

github.com/shahcompbio/hmmcopy_utils

modules/hmmcopy_mapcounter

Description

Input

`meta`
`:map`

`bigwig`
`:file`

Output

`wig`

`meta`
`:map`

`*.wig`
`:file`

`versions_hmmcopy`

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

`hmmcopy`
`:string`

`0.1.1`
`:string`

Topics

`versions`

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

`hmmcopy`
`:string`

`0.1.1`
`:string`

Tools

hmmcopy
GPL v3

maintainer

get in touch

modules/hmmcopy_mapcounter

Description

Input

meta :map

bigwig :file

Output

wig

meta :map

*.wig :file

versions_hmmcopy

${task.process} :string

hmmcopy :string

0.1.1 :string

Topics

versions

${task.process} :string

hmmcopy :string

0.1.1 :string

Tools

hmmcopyGPL v3

maintainer

get in touch

`meta`
`:map`

`bigwig`
`:file`

`wig`

`meta`
`:map`

`*.wig`
`:file`

`versions_hmmcopy`

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

`hmmcopy`
`:string`

`0.1.1`
`:string`

`versions`

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

`hmmcopy`
`:string`

`0.1.1`
`:string`

hmmcopy
GPL v3