modules/gatk4_splitintervals

Split intervals into sub-interval files.

bedgatk4intervalsplitintervals

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

Description

Split intervals into sub-interval files.

Input

name:type

description

pattern

`meta`
`:map`

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

`intervals`
`:file`

Interval file

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fasta`
`:file`

Reference FASTA

*.{fa,fasta}

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`fai`
`:file`

Reference FASTA index

*.fai

`meta4`
`:map`

Groovy Map containing reference information e.g. [ id:‘genome’ ]

`dict`
`:file`

Reference sequence dictionary

*.dict

Output

name:type

description

pattern

`split_intervals`

`meta`
`:map`

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

*.interval_list

`**.interval_list`
`:map`

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

*.interval_list

`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_splitintervals

Description

Input

`meta`
`:map`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

Output

`split_intervals`

`meta`
`:map`

`**.interval_list`
`: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

maintainers

get in touch

modules/gatk4_splitintervals

Description

Input

meta:map

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

Output

split_intervals

meta:map

**.interval_list: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

maintainers

get in touch

`meta`
`:map`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`split_intervals`

`meta`
`:map`

`**.interval_list`
`: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