modules/somalier_relate

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/relate

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 ]

`extract`
`:file`

extract file(s) from Somalier extract

*.somalier

`ped`
`:file`

optional path to a ped or fam file indicating the expected relationships among samples

*.{ped,fam}

`sample_groups`
`:file`

optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line

*.{txt,csv}

Output

name:type

description

pattern

`html`

`meta`
`:file`

html file

*.html

`*.html`
`:file`

html file

*.html

`pairs_tsv`

`meta`
`:file`

html file

*.html

`*.pairs.tsv`
`:file`

tsv file with output stats for pairs of samples

*.pairs.tsv

`samples_tsv`

`meta`
`:file`

html file

*.html

`*.samples.tsv`
`:file`

tsv file with sample-level information

*.samples.tsv

`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_relate

Description

Input

`meta`
`:map`

`extract`
`:file`

`ped`
`:file`

`sample_groups`
`:file`

Output

`html`

`meta`
`:file`

`*.html`
`:file`

`pairs_tsv`

`meta`
`:file`

`*.pairs.tsv`
`:file`

`samples_tsv`

`meta`
`:file`

`*.samples.tsv`
`: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_relate

Description

Input

meta:map

extract:file

ped:file

sample_groups:file

Output

html

meta:file

*.html:file

pairs_tsv

meta:file

*.pairs.tsv:file

samples_tsv

meta:file

*.samples.tsv: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`

`extract`
`:file`

`ped`
`:file`

`sample_groups`
`:file`

`html`

`meta`
`:file`

`*.html`
`:file`

`pairs_tsv`

`meta`
`:file`

`*.pairs.tsv`
`:file`

`samples_tsv`

`meta`
`:file`

`*.samples.tsv`
`: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