modules/gatk4_intervallisttobed

Converts an Picard IntervalList file to a BED file.

bedconversiongatk4interval

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/intervallisttobed

Description

Converts an Picard IntervalList file to a BED file.

Input

name:type

description

pattern

`meta`
`:map`

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

`intervals`
`:file`

IntervalList file

Output

name:type

description

pattern

`bed`

`meta`
`:map`

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

`${prefix}.bed`
`:map`

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

${prefix}.bed

`versions_gatk4`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//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

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
BSD-3-clause

Genome Analysis Toolkit (GATK4)

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_intervallisttobed

Description

Input

`meta`
`:map`

`intervals`
`:file`

Output

`bed`

`meta`
`:map`

`${prefix}.bed`
`:map`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
BSD-3-clause

included in

maintainer

get in touch

modules/gatk4_intervallisttobed

Description

Input

meta:map

intervals:file

Output

bed

meta:map

${prefix}.bed:map

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 BSD-3-clause

included in

maintainer

get in touch

`meta`
`:map`

`intervals`
`:file`

`bed`

`meta`
`:map`

`${prefix}.bed`
`:map`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
BSD-3-clause