modules/gatk4_determinegermlinecontigploidy

Determines the baseline contig ploidy for germline samples given counts data

copy numbercountsdeterminegermlinecontigploidygatk4

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

Description

Determines the baseline contig ploidy for germline samples given counts data

Input

name:type

description

pattern

`meta`
`:map`

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

`counts`
`:file`

One or more count TSV files created with gatk/collectreadcounts

*.tsv

`bed`
`:file`

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

*.bed

`exclude_beds`
`:file`

Optional - One or more bed files containing intervals to exclude from the process

*.bed

`meta2`
`:map`

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

`ploidy_model`
`:directory`

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

`contig_ploidy_table`
`:file`

The contig ploidy priors table

*.tsv

Output

name:type

description

pattern

`calls`

`meta`
`:map`

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

`${prefix}-calls`
`:directory`

A folder containing the calls from the input files

*-calls/

`model`

`meta`
`:map`

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

`${prefix}-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).

*-model/

`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_determinegermlinecontigploidy

Description

Input

`meta`
`:map`

`counts`
`:file`

`bed`
`:file`

`exclude_beds`
`:file`

`meta2`
`:map`

`ploidy_model`
`:directory`

`contig_ploidy_table`
`:file`

Output

`calls`

`meta`
`:map`

`${prefix}-calls`
`:directory`

`model`

`meta`
`:map`

`${prefix}-model`
`: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

maintainer

get in touch

modules/gatk4_determinegermlinecontigploidy

Description

Input

meta:map

counts:file

bed:file

exclude_beds:file

meta2:map

ploidy_model:directory

contig_ploidy_table:file

Output

calls

meta:map

${prefix}-calls:directory

model

meta:map

${prefix}-model: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

maintainer

get in touch

`meta`
`:map`

`counts`
`:file`

`bed`
`:file`

`exclude_beds`
`:file`

`meta2`
`:map`

`ploidy_model`
`:directory`

`contig_ploidy_table`
`:file`

`calls`

`meta`
`:map`

`${prefix}-calls`
`:directory`

`model`

`meta`
`:map`

`${prefix}-model`
`: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