agat/agat_sp_merge_annotations

gene annotations

merge

gff

Description

Merge different gff annotation files into one. It uses the AGAT parser that takes care of
duplicated names and fixes other oddities met in those files.

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

merge

gff

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 v0.3.0 \  
  -main-script target/nextflow/agat/agat_sp_merge_annotations/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--gff -f	file required multiple	Input GTF/GFF file(s).

Name

Type & Properties

--gff

-f

file

required

multiple

Outputs

Name	Type & Properties	Description
--output -o --out	file required output	Output gff3 file where the gene incriminated will be writen.

Name

Type & Properties

--output

-o

--out

file

required

output

Arguments

Name	Type & Properties	Description
--config -c	file	AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. 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