Description

Gathers scattered BQSR recalibration reports into a single file

Input

name:type
description
pattern

meta{:bash}

:map

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

table{:bash}

:file

File(s) containing BQSR table(s)

*.table

Output

name:type
description
pattern

table{:bash}

meta{:bash}

:map

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

*.table{:bash}

:file

File containing joined BQSR table

*.table

versions_gatk4{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

gatk4{:bash}

:string

The name of the tool

gatk --version | sed -n '/GATK.*v/s/.*v//p'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
genomicrelatednessrnadnavarsarek
maintainer
Github user FriederikeHanssen
get in touch
Ask a question on Slack Open an issue on GitHub