modules/ucsc_liftover

convert between genome builds

beducscucsc/liftover

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

Description

convert between genome builds

Input

name:type

description

pattern

`meta`
`:map`

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

`bed`
`:file`

Browser Extensible Data (BED) file

*.{bed}

`chain`
`:file`

Chain file

*.{chain,chain.gz}

Output

name:type

description

pattern

`lifted`

`meta`
`:map`

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

`*.lifted.bed`
`:file`

BED file containing successfully lifted variants

*.{lifted.bed}

`unlifted`

`meta`
`:map`

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

`*.unlifted.bed`
`:file`

BED file containing variants that couldn’t be lifted

*.{unlifted.bed}

`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

Move annotations from one assembly to another

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

modules/ucsc_liftover

Description

Input

`meta`
`:map`

`bed`
`:file`

`chain`
`:file`

Output

`lifted`

`meta`
`:map`

`*.lifted.bed`
`:file`

`unlifted`

`meta`
`:map`

`*.unlifted.bed`
`: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

included in

maintainer

get in touch

modules/ucsc_liftover

Description

Input

meta :map

bed :file

chain :file

Output

lifted

meta :map

*.lifted.bed :file

unlifted

meta :map

*.unlifted.bed :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

included in

maintainer

get in touch

`meta`
`:map`

`bed`
`:file`

`chain`
`:file`

`lifted`

`meta`
`:map`

`*.lifted.bed`
`:file`

`unlifted`

`meta`
`:map`

`*.unlifted.bed`
`: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