modules/gatk4_gatherbqsrreports

Gathers scattered BQSR recalibration reports into a single file

base quality score recalibrationbqsrgatherbqsrreportsgatk4

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

Description

Gathers scattered BQSR recalibration reports into a single file

Input

name:type

description

pattern

`meta`
`:map`

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

`table`
`:file`

File(s) containing BQSR table(s)

*.table

Output

name:type

description

pattern

`table`

`meta`
`:map`

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

`*.table`
`:file`

File containing joined BQSR table

*.table

`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
BSD-3-clause

Genome Analysis Toolkit (GATK4)

gatk.broadinstitute.org/hc/en-us https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_gatherbqsrreports

Description

Input

`meta`
`:map`

`table`
`:file`

Output

`table`

`meta`
`:map`

`*.table`
`: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
BSD-3-clause

included in

maintainer

get in touch

modules/gatk4_gatherbqsrreports

Description

Input

meta:map

table:file

Output

table

meta:map

*.table: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 BSD-3-clause

included in

maintainer

get in touch

`meta`
`:map`

`table`
`:file`

`table`

`meta`
`:map`

`*.table`
`: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
BSD-3-clause