modules/stranger

Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.

STRrepeat_expansionsannotatevcf

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

Description

Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

VCF with repeat expansions

*.{vcf.gz,vcf}

`meta2`
`:map`

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

`variant_catalog`
`:file`

json file with repeat expansion sites to genotype

*.{json}

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

Annotated VCF file

*.{vcf.gz}

`*.vcf.gz`
`:map`

Annotated VCF file

*.{vcf.gz}

`tbi`

`meta`
`:map`

Annotated VCF file

*.{vcf.gz}

`*.vcf.gz.tbi`
`:map`

Index of the annotated VCF file

*.{vcf.gz.tbi}

`versions_stranger`

`${task.process}`
`:string`

The name of the process

`stranger`
`:string`

The name of the tool

`stranger --version | sed 's/stranger, version //g'`
`:eval`

The expression to obtain the version of the tool

`versions_tabix`

`${task.process}`
`:string`

The name of the process

`tabix`
`:string`

The tool name

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`stranger`
`:string`

The name of the tool

`stranger --version | sed 's/stranger, version //g'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`tabix`
`:string`

The tool name

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

The expression to obtain the version of the tool

Tools

stranger
MIT

Annotate VCF files with str variants

github.com/moonso/stranger 10.5281/zenodo.4548873

modules/stranger

Description

Input

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`variant_catalog`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:map`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:map`

`versions_stranger`

`${task.process}`
`:string`

`stranger`
`:string`

`stranger --version | sed 's/stranger, version //g'`
`:eval`

`versions_tabix`

`${task.process}`
`:string`

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`stranger`
`:string`

`stranger --version | sed 's/stranger, version //g'`
`:eval`

`${task.process}`
`:string`

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

Tools

stranger
MIT

included in

maintainer

get in touch

modules/stranger

Description

Input

meta :map

vcf :file

meta2 :map

variant_catalog :file

Output

vcf

meta :map

*.vcf.gz :map

tbi

meta :map

*.vcf.gz.tbi :map

versions_stranger

${task.process} :string

stranger :string

stranger --version | sed 's/stranger, version //g' :eval

versions_tabix

${task.process} :string

tabix :string

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+' :eval

Topics

versions

${task.process} :string

stranger :string

stranger --version | sed 's/stranger, version //g' :eval

${task.process} :string

tabix :string

tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+' :eval

Tools

strangerMIT

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`meta2`
`:map`

`variant_catalog`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:map`

`tbi`

`meta`
`:map`

`*.vcf.gz.tbi`
`:map`

`versions_stranger`

`${task.process}`
`:string`

`stranger`
`:string`

`stranger --version | sed 's/stranger, version //g'`
`:eval`

`versions_tabix`

`${task.process}`
`:string`

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

`versions`

`${task.process}`
`:string`

`stranger`
`:string`

`stranger --version | sed 's/stranger, version //g'`
`:eval`

`${task.process}`
`:string`

`tabix`
`:string`

`tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+'`
`:eval`

stranger
MIT