modules/vcfanno

quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files

vcfbedannotatevariantluatoml

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

Description

quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

query VCF file

*.{vcf, vcf.gz}

`tbi`
`:file`

tabix index file for the query VCF

*.tbi

`specific_resources`
`:map`

A list of sample specific reference files defined in toml config, must also include indices if bgzipped.

`toml`
`:file`

configuration file with reference file basenames

*.toml

`lua`
`:file`

Lua file for custom annotations

*.lua

`resources`
`:map`

List of reference files defined in toml config, must also include indices if bgzipped.

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

*.vcf.gz

`*.vcf.gz`
`:map`

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

*.vcf.gz

`tbi`

`meta`
`:map`

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

*.vcf.gz

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

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

*.vcf.gz.tbi

`versions_vcfanno`

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

The name of the process

`vcfanno`
`:string`

The name of the tool

`vcfanno 2>&1 | sed -n 's/.version $[0-9.]\+$./\1/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

`vcfanno`
`:string`

The name of the tool

`vcfanno 2>&1 | sed -n 's/.version $[0-9.]\+$./\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

github.com/brentp/vcfanno#vcfanno https://github.com/brentp/vcfanno 10.1186/s13059-016-0973-5

modules/vcfanno

Description

Input

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`specific_resources`
`:map`

`toml`
`:file`

`lua`
`:file`

`resources`
`:map`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:map`

`tbi`

`meta`
`:map`

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

`versions_vcfanno`

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

`vcfanno`
`:string`

`vcfanno 2>&1 | sed -n 's/.version \([0-9.]\+\)./\1/p'`
`:eval`

Topics

`versions`

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

`vcfanno`
`:string`

`vcfanno 2>&1 | sed -n 's/.version \([0-9.]\+\)./\1/p'`
`:eval`

Tools

vcfanno

included in

maintainers

get in touch

modules/vcfanno

Description

Input

meta:map

vcf:file

tbi:file

specific_resources:map

toml:file

lua:file

resources:map

Output

vcf

meta:map

*.vcf.gz:map

tbi

meta:map

*.vcf.gz.tbi:map

versions_vcfanno

${task.process}:string

vcfanno:string

vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p':eval

Topics

versions

${task.process}:string

vcfanno:string

vcfanno 2>&1 | sed -n 's/.*version \([0-9.]\+\).*/\1/p':eval

Tools

vcfanno

included in

maintainers

get in touch

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`specific_resources`
`:map`

`toml`
`:file`

`lua`
`:file`

`resources`
`:map`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:map`

`tbi`

`meta`
`:map`

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

`versions_vcfanno`

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

`vcfanno`
`:string`

`vcfanno 2>&1 | sed -n 's/.version \([0-9.]\+\)./\1/p'`
`:eval`

`versions`

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

`vcfanno`
`:string`

`vcfanno 2>&1 | sed -n 's/.version \([0-9.]\+\)./\1/p'`
`:eval`