modules/eigenstratdatabasetools_eigenstratsnpcoverage

Provide the SNP coverage of each individual in an eigenstrat formatted dataset.

coverageeigenstrateigenstratdatabasetoolssnpsnps

https://github.com/nf-core/modules/[...]/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage

Description

Provide the SNP coverage of each individual in an eigenstrat formatted dataset.

Input

name:type

description

pattern

`meta`
`:map`

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

`geno`
`:file`

An Eigenstrat formatted genotype file

*.{geno}

`snp`
`:file`

An Eigenstrat formatted snp file

*.{snp}

`ind`
`:file`

An Eigenstrat formatted individual file

*.{ind}

Output

name:type

description

pattern

`tsv`

`meta`
`:map`

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

`*.tsv`
`:file`

A TSV table with the number of covered SNPs per individual.

*.{tsv}

`json`

`meta`
`:map`

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

`*.json`
`:file`

A json table with the number of covered SNPs per individual.

*.{json}

`versions_eigenstratdatabasetools`

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

The name of the process

`eigenstratdatabasetools`
`:string`

The name of the tool

`eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`eigenstratdatabasetools`
`:string`

The name of the tool

`eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'`
`:eval`

The expression to obtain the version of the tool

Tools

eigenstratdatabasetools
GPL v3

A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases.

github.com/TCLamnidis/EigenStratDatabaseTools/README.md https://github.com/TCLamnidis/EigenStratDatabaseTools

modules/eigenstratdatabasetools_eigenstratsnpcoverage

Description

Input

`meta`
`:map`

`geno`
`:file`

`snp`
`:file`

`ind`
`:file`

Output

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`versions_eigenstratdatabasetools`

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

`eigenstratdatabasetools`
`:string`

`eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'`
`:eval`

Topics

`versions`

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

`eigenstratdatabasetools`
`:string`

`eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'`
`:eval`

Tools

eigenstratdatabasetools
GPL v3

maintainer

get in touch

modules/eigenstratdatabasetools_eigenstratsnpcoverage

Description

Input

meta:map

geno:file

snp:file

ind:file

Output

tsv

meta:map

*.tsv:file

json

meta:map

*.json:file

versions_eigenstratdatabasetools

${task.process}:string

eigenstratdatabasetools:string

eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //':eval

Topics

versions

${task.process}:string

eigenstratdatabasetools:string

eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //':eval

Tools

eigenstratdatabasetools GPL v3

maintainer

get in touch

`meta`
`:map`

`geno`
`:file`

`snp`
`:file`

`ind`
`:file`

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`json`

`meta`
`:map`

`*.json`
`:file`

`versions_eigenstratdatabasetools`

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

`eigenstratdatabasetools`
`:string`

`eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'`
`:eval`

`versions`

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

`eigenstratdatabasetools`
`:string`

`eigenstrat_snp_coverage --version 2>&1 | sed 's/^.*eigenstrat_snp_coverage //'`
`:eval`

eigenstratdatabasetools
GPL v3