modules/ucsc_bedtobigbed

Convert file from bed to bigBed format

bedbigbeducscbedtobigbedconverter

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

Description

Convert file from bed to bigBed format

Input

name:type

description

pattern

`meta`
`:map`

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

`bed`
`:file`

bed file

*.{bed}

`sizes`
`:file`

chromosome sizes file

*.{sizes}

`autosql`
`:file`

autoSql file to describe the columns of the BED file

*.{as}

Output

name:type

description

pattern

`bigbed`

`meta`
`:map`

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

`*.bigBed`
`:file`

bigBed file

*.{bigBed}

`versions_ucsc`

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

The name of the process

`ucsc`
`:string`

The name of the tool

`482`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`ucsc`
`:string`

The name of the tool

`482`
`:string`

The expression to obtain the version of the tool

Tools

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

Convert file from bed to bigBed format

http://hgdownload.cse.ucsc.edu/admin/exe genome.ucsc.edu/goldenPath/help/bigBed

modules/ucsc_bedtobigbed

Description

Input

`meta`
`:map`

`bed`
`:file`

`sizes`
`:file`

`autosql`
`:file`

Output

`bigbed`

`meta`
`:map`

`*.bigBed`
`:file`

`versions_ucsc`

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

`ucsc`
`:string`

`482`
`:string`

Topics

`versions`

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

`ucsc`
`:string`

`482`
`:string`

Tools

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

maintainer

get in touch

modules/ucsc_bedtobigbed

Description

Input

meta :map

bed :file

sizes :file

autosql :file

Output

bigbed

meta :map

*.bigBed :file

versions_ucsc

${task.process} :string

ucsc :string

482 :string

Topics

versions

${task.process} :string

ucsc :string

482 :string

Tools

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

maintainer

get in touch

`meta`
`:map`

`bed`
`:file`

`sizes`
`:file`

`autosql`
`:file`

`bigbed`

`meta`
`:map`

`*.bigBed`
`:file`

`versions_ucsc`

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

`ucsc`
`:string`

`482`
`:string`

`versions`

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

`ucsc`
`:string`

`482`
`:string`

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