modules/bcftools_pluginsplit

Split VCF by sample, creating single- or multi-sample VCFs.

splitvcfgenomics

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

Description

Split VCF by sample, creating single- or multi-sample VCFs.

Input

name:type

description

pattern

`meta`
`:map`

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

`vcf`
`:file`

The VCF file to split

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

`tbi`
`:file`

OPTIONAL - The index of the input VCF/BCF

*.tbi

`samples`
`:file`

A tab-separated file determining which samples should be in which output file column 1: The sample name(s) in the input file column 2: The sample name(s) to use in the output file (use - to keep the original name) column 3: The name of the output file Either this or a groups file should be given

*

`groups`
`:file`

A tab-separated file determining which samples should be in which output file(s) column 1: The sample name(s) in the input file column 2: The sample name(s) to use in the output file (use - to keep the original name) column 3: The name of the output file(s) Either this or a samples file should be given

*

`regions`
`:file`

A BED file containing regions to use

*.bed

`targets`
`:file`

A BED file containing regions to use (but streams rather than index-jumps)

*.bed

Output

name:type

description

pattern

`vcf`

`meta`
`:map`

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

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

The resulting VCF files from the split

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

`tbi`

`meta`
`:map`

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

`*.tbi`
`:file`

TBI file

*.tbi

`csi`

`meta`
`:map`

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

`*.csi`
`:file`

CSI file

*.csi

`versions_bcftools`

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

The process the versions were collected from

`bcftools`
`:string`

The tool name

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

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`bcftools`
`:string`

The tool name

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

The command used to generate the version of the tool

Tools

pluginsplit
MIT

Split VCF by sample, creating single- or multi-sample VCFs.

http://samtools.github.io/bcftools/bcftools http://www.htslib.org/doc/bcftools 10.1093/bioinformatics/btp352

modules/bcftools_pluginsplit

Description

Input

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`samples`
`:file`

`groups`
`:file`

`regions`
`:file`

`targets`
`:file`

Output

`vcf`

`meta`
`:map`

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

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`versions_bcftools`

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

`bcftools`
`:string`

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

Topics

`versions`

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

`bcftools`
`:string`

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

Tools

pluginsplit
MIT

included in

maintainer

get in touch

modules/bcftools_pluginsplit

Description

Input

meta:map

vcf:file

tbi:file

samples:file

groups:file

regions:file

targets:file

Output

vcf

meta:map

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

tbi

meta:map

*.tbi:file

csi

meta:map

*.csi:file

versions_bcftools

${task.process}:string

bcftools:string

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

Topics

versions

${task.process}:string

bcftools:string

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

Tools

pluginsplit MIT

included in

maintainer

get in touch

`meta`
`:map`

`vcf`
`:file`

`tbi`
`:file`

`samples`
`:file`

`groups`
`:file`

`regions`
`:file`

`targets`
`:file`

`vcf`

`meta`
`:map`

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

`tbi`

`meta`
`:map`

`*.tbi`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`versions_bcftools`

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

`bcftools`
`:string`

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

`versions`

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

`bcftools`
`:string`

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

pluginsplit
MIT