Description

Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file

Input

name:type
description
pattern

meta:map

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

]

gxf:file

Annotation file in GFF3/GTF format

*.{gff, gtf}

Output

name:type
description
pattern

output_gff

meta:file

Cleaned annotation file in GFF3 format

*.{gff}

*.agat.gff:file

Cleaned annotation file in GFF3 format

*.{gff}

log

meta:file

Log file of the conversion process

*.{log}

*.log:file

Log file of the conversion process

*.{log}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

agat
GPL v3

AGAT is a toolkit for manipulation and getting information from GFF/GTF files