modules/vcflib_vcffixup

Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.

vcfvcflibvcflib/vcffixupAC/NS/AF

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

Description

Generates a VCF stream where AC and NS have been generated for each record using sample genotypes.

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

Compressed VCF file

*.{.vcf.gz,vcf}

`tbi`
`:file`

Index of VCF file

*.vcf.gz.tbi

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

`*.{vcf,bcf}{,.gz}`
`:file`

Compressed or not VCF or BCF file

*.{vcf,bcf}{,.gz}

`index`

`meta`
`:map`

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

`*.{csi,tbi}`
`:file`

Index file

*.{csi,tbi}

`versions_vcflib`

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

The name of the process

`vcflib`
`:string`

The name of the tool

`1.0.14`
`:string`

The expression to obtain the version of the tool

`versions_bcftools`

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

The process the versions were collected from

`bcftools`
`:string`

The tool name

`bcftools --version | sed '1!d; s/^.*bcftools //'`
`:eval`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`vcflib`
`:string`

The name of the tool

`1.0.14`
`:string`

The expression to obtain the version of the tool

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

The process the versions were collected from

`bcftools`
`:string`

The tool name

`bcftools --version | sed '1!d; s/^.*bcftools //'`
`:eval`

The command used to generate the version of the tool

Tools

vcflib
MIT

Command-line tools for manipulating VCF files

github.com/vcflib/vcflib github.com/vcflib/vcflib#USAGE 10.1101/2021.05.21.445151

bcftools
MITGPL-3.0-or-later

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.

samtools.github.io/bcftools samtools.github.io/bcftools/howtos https://github.com/samtools/bcftools 10.1093/gigascience/giab008

modules/vcflib_vcffixup

Description

Input

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

Output

`vcf`

`meta`
`:map`

`*.{vcf,bcf}{,.gz}`
`:file`

`index`

`meta`
`:map`

`*.{csi,tbi}`
`:file`

`versions_vcflib`

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

`vcflib`
`:string`

`1.0.14`
`:string`

`versions_bcftools`

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

`bcftools`
`:string`

`bcftools --version | sed '1!d; s/^.*bcftools //'`
`:eval`

Topics

`versions`

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

`vcflib`
`:string`

`1.0.14`
`:string`

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

`bcftools`
`:string`

`bcftools --version | sed '1!d; s/^.*bcftools //'`
`:eval`

Tools

vcflib
MIT

bcftools
MITGPL-3.0-or-later

included in

maintainer

get in touch

modules/vcflib_vcffixup

Description

Input

meta :map

vcf :file

tbi :file

Output

vcf

meta :map

*.{vcf,bcf}{,.gz} :file

index

meta :map

*.{csi,tbi} :file

versions_vcflib

${task.process} :string

vcflib :string

1.0.14 :string

versions_bcftools

${task.process} :string

bcftools :string

bcftools --version | sed '1!d; s/^.*bcftools //' :eval

Topics

versions

${task.process} :string

vcflib :string

1.0.14 :string

${task.process} :string

bcftools :string

bcftools --version | sed '1!d; s/^.*bcftools //' :eval

Tools

vcflibMIT

bcftoolsMITGPL-3.0-or-later

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`vcf`

`meta`
`:map`

`*.{vcf,bcf}{,.gz}`
`:file`

`index`

`meta`
`:map`

`*.{csi,tbi}`
`:file`

`versions_vcflib`

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

`vcflib`
`:string`

`1.0.14`
`:string`

`versions_bcftools`

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

`bcftools`
`:string`

`bcftools --version | sed '1!d; s/^.*bcftools //'`
`:eval`

`versions`

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

`vcflib`
`:string`

`1.0.14`
`:string`

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

`bcftools`
`:string`

`bcftools --version | sed '1!d; s/^.*bcftools //'`
`:eval`

vcflib
MIT

bcftools
MITGPL-3.0-or-later