modules/gvcftools_extractvariants

Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.

gvcftoolsextract_variantsextractvariantsgvcfvcf

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

Description

Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.

Input

name:type

description

pattern

`meta`
`:map`

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

`gvcf`
`:file`

GVCF file

*.{g.vcf,gvcf}.gz

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.vcf.gz`
`:file`

Converted variant-only VCF file

*.vcf.gz

`versions_gvcftools`

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

The name of the process

`gvcftools`
`:string`

The name of the tool

`extract_variants --help 2>&1 | sed -n 's/version: //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

`gvcftools`
`:string`

The name of the tool

`extract_variants --help 2>&1 | sed -n 's/version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

gvcftools
MIT

gvcftools is a package of small utilities for creating and analyzing gVCF files

sites.google.com/site/gvcftools/home sites.google.com/site/gvcftools/home/configuration-and-analysis https://github.com/sequencing/gvcftools

modules/gvcftools_extractvariants

Description

Input

`meta`
`:map`

`gvcf`
`:file`

Output

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`versions_gvcftools`

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

`gvcftools`
`:string`

`extract_variants --help 2>&1 | sed -n 's/version: //p'`
`:eval`

Topics

`versions`

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

`gvcftools`
`:string`

`extract_variants --help 2>&1 | sed -n 's/version: //p'`
`:eval`

Tools

gvcftools
MIT

maintainer

get in touch

modules/gvcftools_extractvariants

Description

Input

meta:map

gvcf:file

Output

vcf

meta:map

*.vcf.gz:file

versions_gvcftools

${task.process}:string

gvcftools:string

extract_variants --help 2>&1 | sed -n 's/version: //p':eval

Topics

versions

${task.process}:string

gvcftools:string

extract_variants --help 2>&1 | sed -n 's/version: //p':eval

Tools

gvcftools MIT

maintainer

get in touch

`meta`
`:map`

`gvcf`
`:file`

`vcf`

`meta`
`:map`

`*.vcf.gz`
`:file`

`versions_gvcftools`

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

`gvcftools`
`:string`

`extract_variants --help 2>&1 | sed -n 's/version: //p'`
`:eval`

`versions`

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

`gvcftools`
`:string`

`extract_variants --help 2>&1 | sed -n 's/version: //p'`
`:eval`

gvcftools
MIT