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{:bash}

:map

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

counts{:bash}

:file

Contains count data of repetitive regions.

meta2{:bash}

:map

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

ref{:bash}

:file

An input nucleotide fasta file.

Output

name:type
description
pattern

intervals{:bash}

meta{:bash}

:map

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

${output}{:bash}

:file

intervals

versions_windowmasker{:bash}

${task.process}{:bash}

:string

The name of the process

windowmasker{:bash}

:string

The name of the tool

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

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

windowmasker{:bash}

:string

The name of the tool

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

: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
maintainer
Github user DLBPointon
get in touch
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