modules/somalier_ancestry

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/ancestry

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 ]

`query_somalier_files`
`:file`

Set of somalier files for query samples. Obtained via somalier extract.

*.{somalier}

`meta2`
`:map`

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

`labels_tsv`
`:file`

TSV for labelled samples. e.g. Somalier labels for 1kg https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv

*.{tsv}

`labelled_somalier_files`
`:file`

Set of somalier files for labelled samples. e.g. Somalier files for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1

*.{somalier}

Output

name:type

description

pattern

`tsv`

`meta`
`:map`

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

`*.somalier-ancestry.tsv`
`:file`

TSV with ancestry information for query and labelled samples.

*.somalier-ancestry.tsv

`html`

`meta`
`:map`

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

`*.somalier-ancestry.html`
`:file`

html file with ancestry information for query and labelled samples.

*.somalier-ancestry.html

`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 10.1186/s13073-020-00761-2

modules/somalier_ancestry

Description

Input

`meta`
`:map`

`query_somalier_files`
`:file`

`meta2`
`:map`

`labels_tsv`
`:file`

`labelled_somalier_files`
`:file`

Output

`tsv`

`meta`
`:map`

`*.somalier-ancestry.tsv`
`:file`

`html`

`meta`
`:map`

`*.somalier-ancestry.html`
`: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

maintainer

get in touch

modules/somalier_ancestry

Description

Input

meta :map

query_somalier_files :file

meta2 :map

labels_tsv :file

labelled_somalier_files :file

Output

tsv

meta :map

*.somalier-ancestry.tsv :file

html

meta :map

*.somalier-ancestry.html :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

somalierMIT

maintainer

get in touch

`meta`
`:map`

`query_somalier_files`
`:file`

`meta2`
`:map`

`labels_tsv`
`:file`

`labelled_somalier_files`
`:file`

`tsv`

`meta`
`:map`

`*.somalier-ancestry.tsv`
`:file`

`html`

`meta`
`:map`

`*.somalier-ancestry.html`
`: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