agat/agat_convert_sp_gxf2gxf

gene annotations

GFF conversion

Description

This script fixes and/or standardizes any GTF/GFF file into full sorted
GTF/GFF file. It AGAT parser removes duplicate features, fixes
duplicated IDs, adds missing ID and/or Parent attributes, deflates
factorized attributes (attributes with several parents are duplicated
with uniq ID), add missing features when possible (e.g. add exon if only
CDS described, add UTR if CDS and exon described), fix feature locations
(e.g. check exon is embedded in the parent features mRNA, gene), etc...

All AGAT's scripts with the sp prefix use the AGAT parser, before to
perform any supplementary task. So, it is not necessary to run this
script prior the use of any other sp script.

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

GFF conversion

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.gff"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--gxf -g --gtf --gff	file required	String - Input GTF/GFF file. Compressed file with .gz extension is accepted.

Name

Type & Properties

--gxf

-g

--gtf

--gff

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	String - Output GFF file. If no output file is specified, the output will be written to STDOUT.

Name

Type & Properties

--output

-o

file

required

output

Arguments

Name	Type & Properties	Description
--config -c	file	String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

Name

Type & Properties

--config

-c

file