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`
`:map`

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

`fasta`
`:file`

Input genome fasta file

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 gc content 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_gccounter

Description

Input

`meta`
`:map`

`fasta`
`: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

maintainers

get in touch

modules/hmmcopy_gccounter

Description

Input

meta :map

fasta :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

maintainers

get in touch

`meta`
`:map`

`fasta`
`: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