modules/somalier_extract

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

relatednessQCbamcramvcfgvcfancestryidentitykinshipinformative sitesfamily

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

Description

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file

`input_index`
`:file`

index file of the input data, e.g., bam.bai, cram.crai

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:‘hg38’ ]

`fasta`
`:file`

The reference fasta file

*.{fasta,fna,fas,fa}

`meta3`
`:map`

Groovy Map containing reference information e.g. [ id:‘hg38’ ]

`fai`
`:file`

FASTA index file

*.fai

`meta4`
`:map`

Groovy Map containing sites information e.g. [ id:‘hg38’ ]

`sites`
`:file`

sites file in VCF format which can be taken from https://github.com/brentp/somalier

*.vcf.gz

Output

name:type

description

pattern

`extract`

`meta`
`:map`

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

`*.somalier`
`:file`

binary output file based on extracted sites

*.{somalier}

`versions_somalier`

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

The name of the process

`somalier`
`:string`

The name of the tool

`somalier 2>&1 | sed -n 's/.version: $[0-9.]$.*/\1/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

`somalier`
`:string`

The name of the tool

`somalier 2>&1 | sed -n 's/.version: $[0-9.]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

somalier
MIT

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

github.com/brentp/somalier github.com/brentp/somalier/blob/master/README.md https://github.com/brentp/somalier 10.1186/s13073-020-00761-2

modules/somalier_extract

Description

Input

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`sites`
`:file`

Output

`extract`

`meta`
`:map`

`*.somalier`
`:file`

`versions_somalier`

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

`somalier`
`:string`

`somalier 2>&1 | sed -n 's/.version: \([0-9.]\).*/\1/p'`
`:eval`

Topics

`versions`

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

`somalier`
`:string`

`somalier 2>&1 | sed -n 's/.version: \([0-9.]\).*/\1/p'`
`:eval`

Tools

somalier
MIT

maintainers

get in touch

modules/somalier_extract

Description

Input

meta:map

input:file

input_index:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

sites:file

Output

extract

meta:map

*.somalier:file

versions_somalier

${task.process}:string

somalier:string

somalier 2>&1 | sed -n 's/.*version: \([0-9.]*\).*/\1/p':eval

Topics

versions

${task.process}:string

somalier:string

somalier 2>&1 | sed -n 's/.*version: \([0-9.]*\).*/\1/p':eval

Tools

somalier MIT

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`sites`
`:file`

`extract`

`meta`
`:map`

`*.somalier`
`:file`

`versions_somalier`

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

`somalier`
`:string`

`somalier 2>&1 | sed -n 's/.version: \([0-9.]\).*/\1/p'`
`:eval`

`versions`

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

`somalier`
`:string`

`somalier 2>&1 | sed -n 's/.version: \([0-9.]\).*/\1/p'`
`:eval`

somalier
MIT