modules/windowmasker_ustat

A program to take a counts file and creates a file of genomic co-ordinates to be masked.

fastaintervalwindowmasker

https://github.com/nf-core/modules/[...]/modules/nf-core/windowmasker/ustat

Description

A program to take a counts file and creates a file of genomic co-ordinates to be masked.

Input

name:type

description

pattern

`meta`
`:map`

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

`counts`
`:file`

Contains count data of repetitive regions.

`meta2`
`:map`

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

`ref`
`:file`

An input nucleotide fasta file.

Output

name:type

description

pattern

`intervals`

`meta`
`:map`

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

`${output}`
`:file`

intervals

`versions_windowmasker`

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

The name of the process

`windowmasker`
`:string`

The name of the tool

`windowmasker -version-full | head -n 1 | sed 's/^.windowmasker. //; s/ .\$//'`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`windowmasker`
`:string`

The name of the tool

`windowmasker -version-full | head -n 1 | sed 's/^.windowmasker. //; s/ .\$//'`
`:eval`

The expression to obtain the version of the tool

Tools

windowmasker
MIT

A program to mask highly repetitive and low complexity DNA sequences within a genome.

github.com/ncbi/ncbi-cxx-toolkit-public ncbi.github.io/cxx-toolkit

modules/windowmasker_ustat

Description

Input

`meta`
`:map`

`counts`
`:file`

`meta2`
`:map`

`ref`
`:file`

Output

`intervals`

`meta`
`:map`

`${output}`
`:file`

`versions_windowmasker`

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

`windowmasker`
`:string`

`windowmasker -version-full | head -n 1 | sed 's/^.windowmasker. //; s/ .\$//'`
`:string`

Topics

`versions`

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

`windowmasker`
`:string`

`windowmasker -version-full | head -n 1 | sed 's/^.windowmasker. //; s/ .\$//'`
`:eval`

Tools

windowmasker
MIT

maintainer

get in touch

modules/windowmasker_ustat

Description

Input

meta:map

counts:file

meta2:map

ref:file

Output

intervals

meta:map

${output}:file

versions_windowmasker

${task.process}:string

windowmasker:string

windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\$//':string

Topics

versions

${task.process}:string

windowmasker:string

windowmasker -version-full | head -n 1 | sed 's/^.*windowmasker. //; s/ .*\$//':eval

Tools

windowmasker MIT

maintainer

get in touch

`meta`
`:map`

`counts`
`:file`

`meta2`
`:map`

`ref`
`:file`

`intervals`

`meta`
`:map`

`${output}`
`:file`

`versions_windowmasker`

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

`windowmasker`
`:string`

`windowmasker -version-full | head -n 1 | sed 's/^.windowmasker. //; s/ .\$//'`
`:string`

`versions`

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

`windowmasker`
`:string`

`windowmasker -version-full | head -n 1 | sed 's/^.windowmasker. //; s/ .\$//'`
`:eval`

windowmasker
MIT