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 container 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 output WorkingDirectory (used for the orthofinder resume function)

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainer
Github user GallVp
get in touch
Ask a question on Slack Open an issue on GitHub