modules/hmmcopy_gccounter

gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference

hmmcopygccountercnv

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

Description

gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`fasta{:bash}`
`:file`

Input genome fasta file

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 gc content 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_gccounter

Description

Input

`meta{:bash}`
`:map`

`fasta{:bash}`
`:file`

Output

`wig{:bash}`

`meta{:bash}`
`:map`

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

`versions{:bash}`

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

Tools

hmmcopy
GPL v3

maintainers

get in touch

modules/hmmcopy_gccounter

Description

Input

meta{:bash}:map

fasta{:bash}:file

Output

wig{:bash}

meta{:bash}:map

*.wig{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

hmmcopy GPL v3

maintainers

get in touch

`meta{:bash}`
`:map`

`fasta{:bash}`
`:file`

`wig{:bash}`

`meta{:bash}`
`:map`

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

`versions{:bash}`

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

hmmcopy
GPL v3