modules/snpsift_dbnsfp

The dbNSFP is an integrated database of functional predictions from multiple algorithms

variant callingdbnsfpsnpsiftcancer genomicspredictions

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

Description

The dbNSFP is an integrated database of functional predictions from multiple algorithms

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

VCF file

*.{vcf, vcf.gz}

`vcf_tbi`
`:file`

Tabix file for compressed vcf provided

*.{tbi}

`meta2`
`:map`

Groovy map containing sample information regarding database provided

`database`
`:file`

Database for use to annotate

*.{vcf/vcf.gz}

`dbs_tbi`
`:file`

Tabix file for compressed database provided

*.{tbi}

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf`
`:file`

Variant Calling File annotated

*.{vcf}

`versions_snpsift`

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

The name of the process

`snpsift`
`:string`

The name of the tool

`SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`snpsift`
`:string`

The name of the tool

`SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?'`
`:eval`

The expression to obtain the version of the tool

Tools

snpsift
MIT

SnpSift is a toolbox that allows you to filter and manipulate annotated files

pcingola.github.io/SnpEff/ss_introduction pcingola.github.io/SnpEff/ss_dbnsfp https://github.com/pcingola/SnpEff 10.3389/fgene.2012.00035

modules/snpsift_dbnsfp

Description

Input

`meta`
`:map`

`vcf`
`:file`

`vcf_tbi`
`:file`

`meta2`
`:map`

`database`
`:file`

`dbs_tbi`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_snpsift`

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

`snpsift`
`:string`

`SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?'`
`:eval`

Topics

`versions`

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

`snpsift`
`:string`

`SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?'`
`:eval`

Tools

snpsift
MIT

maintainer

get in touch

modules/snpsift_dbnsfp

Description

Input

meta :map

vcf :file

vcf_tbi :file

meta2 :map

database :file

dbs_tbi :file

Output

vcf

meta :map

*.vcf :file

versions_snpsift

${task.process} :string

snpsift :string

SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?' :eval

Topics

versions

${task.process} :string

snpsift :string

SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?' :eval

Tools

snpsiftMIT

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`vcf_tbi`
`:file`

`meta2`
`:map`

`database`
`:file`

`dbs_tbi`
`:file`

`vcf`

`meta`
`:map`

`*.vcf`
`:file`

`versions_snpsift`

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

`snpsift`
`:string`

`SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?'`
`:eval`

`versions`

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

`snpsift`
`:string`

`SnpSift -version 2>&1 | grep -oE '[0-9]+\.[0-9]+[a-z]?'`
`:eval`

snpsift
MIT