modules/genmap_map

create mappability files for a genome

mappabilityindexfastabedgraphcsvwig

https://github.com/nf-core/modules/[...]/modules/nf-core/genmap/map

Description

create mappability files for a genome

Input

name:type

description

pattern

`meta`
`:map`

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

`index`
`:directory`

index directory

`meta2`
`:map`

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

`regions`
`:file`

optional - a bed file with regions to define the mappability off

*.bed

Output

name:type

description

pattern

`wig`

`meta`
`:map`

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

`*.wig`
`:file`

genmap wig mappability file

*.wig

`bedgraph`

`meta`
`:map`

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

`*.bedgraph`
`:file`

genmap bedgraph mappability file

*.bedgraph

`txt`

`meta`
`:map`

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

`*.txt`
`:file`

genmap text mappability file

*.txt

`csv`

`meta`
`:map`

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

`*.csv`
`:file`

genmap csv mappability file

*.csv

`versions_genmap`

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

The name of the process

`genmap`
`:string`

The name of the tool

`genmap --version |& sed -n 's/GenMap version: //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`genmap`
`:string`

The name of the tool

`genmap --version |& sed -n 's/GenMap version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

genmap
BSD-3-Clause

Ultra-fast computation of genome mappability.

github.com/cpockrandt/genmap 10.1093/bioinformatics/btaa222

modules/genmap_map

Description

Input

`meta`
`:map`

`index`
`:directory`

`meta2`
`:map`

`regions`
`:file`

Output

`wig`

`meta`
`:map`

`*.wig`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedgraph`
`:file`

`txt`

`meta`
`:map`

`*.txt`
`:file`

`csv`

`meta`
`:map`

`*.csv`
`:file`

`versions_genmap`

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

`genmap`
`:string`

`genmap --version |& sed -n 's/GenMap version: //p'`
`:eval`

Topics

`versions`

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

`genmap`
`:string`

`genmap --version |& sed -n 's/GenMap version: //p'`
`:eval`

Tools

genmap
BSD-3-Clause

maintainers

get in touch

modules/genmap_map

Description

Input

meta:map

index:directory

meta2:map

regions:file

Output

wig

meta:map

*.wig:file

bedgraph

meta:map

*.bedgraph:file

txt

meta:map

*.txt:file

csv

meta:map

*.csv:file

versions_genmap

${task.process}:string

genmap:string

genmap --version |& sed -n 's/GenMap version: //p':eval

Topics

versions

${task.process}:string

genmap:string

genmap --version |& sed -n 's/GenMap version: //p':eval

Tools

genmap BSD-3-Clause

maintainers

get in touch

`meta`
`:map`

`index`
`:directory`

`meta2`
`:map`

`regions`
`:file`

`wig`

`meta`
`:map`

`*.wig`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedgraph`
`:file`

`txt`

`meta`
`:map`

`*.txt`
`:file`

`csv`

`meta`
`:map`

`*.csv`
`:file`

`versions_genmap`

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

`genmap`
`:string`

`genmap --version |& sed -n 's/GenMap version: //p'`
`:eval`

`versions`

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

`genmap`
`:string`

`genmap --version |& sed -n 's/GenMap version: //p'`
`:eval`

genmap
BSD-3-Clause