modules/ucsc_bedclip

Remove lines from bed file that refer to off-chromosome locations.

bedgenomicsucsc

https://github.com/nf-core/modules/[...]/modules/nf-core/ucsc/bedclip

Description

Remove lines from bed file that refer to off-chromosome locations.

Input

name:type

description

pattern

`meta`
`:map`

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

`bedgraph`
`:file`

bedGraph file

*.{bedgraph}

`sizes`
`:file`

Chromosome sizes file

Output

name:type

description

pattern

`bedgraph`

`meta`
`:map`

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

`*.bedGraph`
`:file`

bedGraph file

*.{bedgraph}

`versions_ucsc`

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

The process the versions were collected from

`ucsc`
`:string`

The tool name

`482`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`ucsc`
`:string`

The tool name

`482`
`:eval`

The expression to obtain the version of the tool

Tools

ucsc
varies; see http://genome.ucsc.edu/license

Remove lines from bed file that refer to off-chromosome locations.

http://hgdownload.cse.ucsc.edu/admin/exe

modules/ucsc_bedclip

Description

Input

`meta`
`:map`

`bedgraph`
`:file`

`sizes`
`:file`

Output

`bedgraph`

`meta`
`:map`

`*.bedGraph`
`:file`

`versions_ucsc`

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

`ucsc`
`:string`

`482`
`:eval`

Topics

`versions`

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

`ucsc`
`:string`

`482`
`:eval`

Tools

ucsc
varies; see http://genome.ucsc.edu/license

included in

maintainer

get in touch

modules/ucsc_bedclip

Description

Input

meta:map

bedgraph:file

sizes:file

Output

bedgraph

meta:map

*.bedGraph:file

versions_ucsc

${task.process}:string

ucsc:string

482:eval

Topics

versions

${task.process}:string

ucsc:string

482:eval

Tools

ucsc varies; see http://genome.ucsc.edu/license

included in

maintainer

get in touch

`meta`
`:map`

`bedgraph`
`:file`

`sizes`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedGraph`
`:file`

`versions_ucsc`

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

`ucsc`
`:string`

`482`
`:eval`

`versions`

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

`ucsc`
`:string`

`482`
`:eval`

ucsc
varies; see http://genome.ucsc.edu/license