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{:bash}`
`:map`

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

`bigwig{:bash}`
`:file`

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

*.wig

Output

name:type

description

pattern

`wig{:bash}`

`meta{:bash}`
`:map`

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

`*.wig{:bash}`
`:file`

wig file containing mappability of each window of the genome

*.wig

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

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{:bash}`
`:map`

`bigwig{:bash}`
`:file`

Output

`wig{:bash}`

`meta{:bash}`
`:map`

`*.wig{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

hmmcopy
GPL v3

maintainer

get in touch

modules/hmmcopy_mapcounter

Description

Input

meta{:bash}:map

bigwig{:bash}:file

Output

wig{:bash}

meta{:bash}:map

*.wig{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

hmmcopy GPL v3

maintainer

get in touch

`meta{:bash}`
`:map`

`bigwig{:bash}`
`:file`

`wig{:bash}`

`meta{:bash}`
`:map`

`*.wig{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

hmmcopy
GPL v3