modules/snpeff_snpeff

Genetic variant annotation and functional effect prediction toolbox

annotationeffect predictionsnpeffvariantvcf

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

Description

Genetic variant annotation and functional effect prediction toolbox

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

vcf to annotate

`db`
`:string`

which db to annotate with

`meta2`
`:map`

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

`cache`
`:file`

path to snpEff cache (optional)

Output

name:type

description

pattern

`vcf`

`meta`
`:file`

annotated vcf

*.ann.vcf

`*.ann.vcf`
`:file`

annotated vcf

*.ann.vcf

`report`

`meta`
`:file`

annotated vcf

*.ann.vcf

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

The process

`snpeff`
`:string`

The tool name

`*.csv`
`:file`

snpEff report csv file

*.csv

`summary_html`

`meta`
`:file`

annotated vcf

*.ann.vcf

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

The process

`snpeff`
`:string`

The tool name

`*.html`
`:file`

snpEff summary statistics in html file

*.html

`genes_txt`

`meta`
`:file`

annotated vcf

*.ann.vcf

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

The process

`snpeff`
`:string`

The tool name

`*.genes.txt`
`:file`

txt (tab separated) file having counts of the number of variants affecting each transcript and gene

*.genes.txt

`versions_snpeff`

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

The process the versions were collected from

`snpeff`
`:string`

The tool name

`snpEff -version 2>&1 | cut -f 2 -d ' '`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`multiqc_files`

`meta`
`:file`

annotated vcf

*.ann.vcf

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

The process

`snpeff`
`:string`

The tool name

`*.csv`
`:file`

snpEff report csv file

*.csv

`meta`
`:file`

annotated vcf

*.ann.vcf

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

The process

`snpeff`
`:string`

The tool name

`*.html`
`:file`

snpEff summary statistics in html file

*.html

`meta`
`:file`

annotated vcf

*.ann.vcf

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

The process

`snpeff`
`:string`

The tool name

`*.genes.txt`
`:file`

txt (tab separated) file having counts of the number of variants affecting each transcript and gene

*.genes.txt

`versions`

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

The process the versions were collected from

`snpeff`
`:string`

The tool name

`snpEff -version 2>&1 | cut -f 2 -d ' '`
`:string`

The command used to generate the version of the tool

Tools

snpeff
MIT

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).

pcingola.github.io/SnpEff pcingola.github.io/SnpEff/se_introduction

modules/snpeff_snpeff

Description

Input

meta:map

vcf:file

db:string

meta2:map

cache:file

Output

vcf

meta:file

*.ann.vcf:file

report

meta:file

${task.process}:string

snpeff:string

*.csv:file

summary_html

meta:file

${task.process}:string

snpeff:string

*.html:file

genes_txt

meta:file

${task.process}:string

snpeff:string

*.genes.txt:file

versions_snpeff

${task.process}:string

snpeff:string

snpEff -version 2>&1 | cut -f 2 -d ' ':string

Topics

multiqc_files

meta:file

${task.process}:string

snpeff:string

*.csv:file

meta:file

${task.process}:string

snpeff:string

*.html:file

meta:file

${task.process}:string

snpeff:string

*.genes.txt:file

versions

${task.process}:string

snpeff:string

snpEff -version 2>&1 | cut -f 2 -d ' ':string

Tools

snpeff MIT

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`db`
`:string`

`meta2`
`:map`

`cache`
`:file`

`vcf`

`meta`
`:file`

`*.ann.vcf`
`:file`

`report`

`meta`
`:file`

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

`snpeff`
`:string`

`*.csv`
`:file`

`summary_html`

`meta`
`:file`

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

`snpeff`
`:string`

`*.html`
`:file`

`genes_txt`

`meta`
`:file`

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

`snpeff`
`:string`

`*.genes.txt`
`:file`

`versions_snpeff`

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

`snpeff`
`:string`

`snpEff -version 2>&1 | cut -f 2 -d ' '`
`:string`

`multiqc_files`

`meta`
`:file`

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

`snpeff`
`:string`

`*.csv`
`:file`

`meta`
`:file`

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

`snpeff`
`:string`

`*.html`
`:file`

`meta`
`:file`

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

`snpeff`
`:string`

`*.genes.txt`
`:file`

`versions`

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

`snpeff`
`:string`

`snpEff -version 2>&1 | cut -f 2 -d ' '`
`:string`

snpeff
MIT