modules/gatk4_germlinecnvcaller

Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.

gatkgermline contig ploidygermlinecnvcaller

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

Description

Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy.

Input

name:type

description

pattern

`meta`
`:map`

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

`tsv`
`:file`

One or more count TSV files created with gatk/collectreadcounts

*.tsv

`intervals`
`:file`

Optional - A bed file containing the intervals to include in the process

*.bed

`ploidy`
`:directory`

Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode

*-calls

`model`
`:directory`

Optional - directory containing the model produced by germlinecnvcaller cohort mode

*-cnv-model/*-model

Output

name:type

description

pattern

`cohortcalls`

`meta`
`:map`

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

`-cnv-model/-calls`
`:directory`

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-model/*-calls

`cohortmodel`

`meta`
`:map`

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

`-cnv-model/-model`
`:directory`

Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode

*-cnv-model/*-model

`casecalls`

`meta`
`:map`

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

`-cnv-calls/-calls`
`:directory`

Tar gzipped directory containing calls produced by germlinecnvcaller case mode

*-cnv-calls/*-calls

`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_germlinecnvcaller

Description

Input

`meta`
`:map`

`tsv`
`:file`

`intervals`
`:file`

`ploidy`
`:directory`

`model`
`:directory`

Output

`cohortcalls`

`meta`
`:map`

`-cnv-model/-calls`
`:directory`

`cohortmodel`

`meta`
`:map`

`-cnv-model/-model`
`:directory`

`casecalls`

`meta`
`:map`

`-cnv-calls/-calls`
`:directory`

`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_germlinecnvcaller

Description

Input

meta:map

tsv:file

intervals:file

ploidy:directory

model:directory

Output

cohortcalls

meta:map

*-cnv-model/*-calls:directory

cohortmodel

meta:map

*-cnv-model/*-model:directory

casecalls

meta:map

*-cnv-calls/*-calls:directory

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`

`tsv`
`:file`

`intervals`
`:file`

`ploidy`
`:directory`

`model`
`:directory`

`cohortcalls`

`meta`
`:map`

`-cnv-model/-calls`
`:directory`

`cohortmodel`

`meta`
`:map`

`-cnv-model/-model`
`:directory`

`casecalls`

`meta`
`:map`

`-cnv-calls/-calls`
`:directory`

`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