modules/gatk4_postprocessgermlinecnvcalls

Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

copy numbergatk4postprocessgermlinecnvcalls

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

Description

Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios

Input

name:type

description

pattern

`meta`
`:map`

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

`calls`
`:directory`

A folder containing the calls from the input files

*-cnv-calls/*-calls

`model`
`:directory`

A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process).

*-cnv-model/*-model

`ploidy`
`:directory`

Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode.

*-calls/

Output

name:type

description

pattern

`intervals`

`meta`
`:map`

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

`*_genotyped_intervals.vcf.gz`
`:file`

Intervals VCF file

*.vcf.gz

`segments`

`meta`
`:map`

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

`*_genotyped_segments.vcf.gz`
`:file`

Segments VCF file

*.vcf.gz

`denoised`

`meta`
`:map`

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

`*_denoised.vcf.gz`
`:file`

Denoised copy ratio file

*.vcf.gz

`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/articles/360037593411-PostprocessGermlineCNVCalls 10.1158/1538-7445.AM2017-3590

modules/gatk4_postprocessgermlinecnvcalls

Description

Input

`meta`
`:map`

`calls`
`:directory`

`model`
`:directory`

`ploidy`
`:directory`

Output

`intervals`

`meta`
`:map`

`*_genotyped_intervals.vcf.gz`
`:file`

`segments`

`meta`
`:map`

`*_genotyped_segments.vcf.gz`
`:file`

`denoised`

`meta`
`:map`

`*_denoised.vcf.gz`
`: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

maintainer

get in touch

modules/gatk4_postprocessgermlinecnvcalls

Description

Input

meta :map

calls :directory

model :directory

ploidy :directory

Output

intervals

meta :map

*_genotyped_intervals.vcf.gz :file

segments

meta :map

*_genotyped_segments.vcf.gz :file

denoised

meta :map

*_denoised.vcf.gz :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

gatk4Apache-2.0

included in

maintainer

get in touch

`meta`
`:map`

`calls`
`:directory`

`model`
`:directory`

`ploidy`
`:directory`

`intervals`

`meta`
`:map`

`*_genotyped_intervals.vcf.gz`
`:file`

`segments`

`meta`
`:map`

`*_genotyped_segments.vcf.gz`
`:file`

`denoised`

`meta`
`:map`

`*_denoised.vcf.gz`
`: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