Description

OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

fastas{:bash}

:list

Input fasta files

*.{fa,faa,fasta,fas,pep}

meta2{:bash}

:map

Groovy Map containing a name e.g. [ id:'folder1' ]

prior_run{:bash}

:directory

A folder containing a previous WorkingDirectory from OrthoFinder.

Output

name:type
description
pattern

orthofinder{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

$prefix{:bash}

:directory

OrthoFinder output directory

working{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

$prefix/WorkingDirectory{:bash}

:directory

OrthoFinder WorkingDirectory (used for the resume function)

versions_orthofinder{:bash}

${task.process}{:bash}

:string

The name of the process

orthofinder{:bash}

:string

The name of the tool

NO_COLOR=1 orthofinder --version | cut -d 'v' -f2 | perl -pe 's/\e\[[0-9;]*m//g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

orthofinder{:bash}

:string

The name of the tool

NO_COLOR=1 orthofinder --version | cut -d 'v' -f2 | perl -pe 's/\e\[[0-9;]*m//g'{:bash}

:eval

The expression to obtain the version of the tool

Tools

orthofinder
GPL v3

Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!

github.com/davidemms/OrthoFinder 10.1186/s13059-019-1832-y
included in
genomeqc
maintainers
Github user GallVp
Github user chriswyatt1
get in touch
Ask a question on Slack Open an issue on GitHub