modules/gatk4_createsomaticpanelofnormals

Create a panel of normals constraining germline and artifactual sites for use with mutect2.

createsomaticpanelofnormalsgatk4panelofnormals

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

Description

Create a panel of normals constraining germline and artifactual sites for use with mutect2.

Input

name:type

description

pattern

`meta`
`:map`

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

`genomicsdb`
`:file`

GenomicsDB database

`meta2`
`:map`

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

`fasta`
`:file`

The reference fasta file

*.fasta

`meta3`
`:map`

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

`fai`
`:file`

Index of reference fasta file

*.fasta.fai

`meta4`
`:map`

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

`dict`
`:file`

GATK sequence dictionary

*.dict

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

A Groovy map containing sample information

`*.vcf.gz`
`:file`

panel of normal as compressed vcf file

*.vcf.gz

`tbi`

`meta`
`:map`

A Groovy map containing sample information

`*.tbi`
`:file`

Tabix index of vcf file

*vcf.gz.tbi

`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

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_createsomaticpanelofnormals

Description

Input

`meta`
`:map`

`genomicsdb`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`: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

included in

maintainer

get in touch

modules/gatk4_createsomaticpanelofnormals

Description

Input

meta:map

genomicsdb:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.tbi: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

included in

maintainer

get in touch

`meta`
`:map`

`genomicsdb`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`tbi`

`meta`
`:map`

`*.tbi`
`: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`