modules/gatk4_preprocessintervals

Prepares bins for coverage collection.

bedgatk4intervalpreprocessintervals

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

Description

Prepares bins for coverage collection.

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

The reference fasta file

*.fasta

`meta2`
`:map`

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

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`meta3`
`:map`

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

`dict`
`:file`

GATK sequence dictionary

*.dict

`meta4`
`:map`

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

`intervals`
`:file`

Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional)

*.{bed,interval_list}

`meta5`
`:map`

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

`exclude_intervals`
`:file`

Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional)

*.{bed,interval_list}

Output

name:type

description

pattern

`interval_list`

`meta`
`:map`

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

`${prefix}.interval_list`
`:file`

Processed interval list file

*.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
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

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

modules/gatk4_preprocessintervals

Description

Input

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`fai`
`:file`

`meta3`
`:map`

`dict`
`:file`

`meta4`
`:map`

`intervals`
`:file`

`meta5`
`:map`

`exclude_intervals`
`:file`

Output

`interval_list`

`meta`
`:map`

`${prefix}.interval_list`
`:file`

`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
Apache-2.0

included in

maintainers

get in touch

modules/gatk4_preprocessintervals

Description

Input

meta:map

fasta:file

meta2:map

fai:file

meta3:map

dict:file

meta4:map

intervals:file

meta5:map

exclude_intervals:file

Output

interval_list

meta:map

${prefix}.interval_list:file

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 Apache-2.0

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`fai`
`:file`

`meta3`
`:map`

`dict`
`:file`

`meta4`
`:map`

`intervals`
`:file`

`meta5`
`:map`

`exclude_intervals`
`:file`

`interval_list`

`meta`
`:map`

`${prefix}.interval_list`
`:file`

`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
Apache-2.0