Description

Provides different type of statistics in text format from a GFF/GTF annotation file

Input

name:type
description
pattern

meta{:bash}

:map

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

gff{:bash}

:file

Annotation file in GFF3/GTF format

*.{gff, gtf}

Output

name:type
description
pattern

stats_txt{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*.txt{:bash}

:file

Output of Statistics execution

*.{txt}

versions_agat{:bash}

${task.process}{:bash}

:string

The name of the process

agat{:bash}

:string

The name of the tool

agat --version | sed 's/v//'{: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

agat{:bash}

:string

The name of the tool

agat --version | sed 's/v//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

agat
GPL v3

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

github.com/NBISweden/AGAT agat.readthedocs.io https://github.com/NBISweden/AGAT 10.5281/zenodo.3552717
included in
genomeqc
maintainers
Github user toniher
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub