agat/agat_sp_add_introns

gene annotations

GTF conversion

Description

Add intronic elements to a gtf/gff file without intron features.

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

GTF 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 v0.4.0 \  
  -main-script target/nextflow/agat/agat_sp_add_introns/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--gff -f --ref --reffile	file required	Input GTF/GFF file.

Name

Type & Properties

--gff

-f

--ref

--reffile

file

required

Outputs

Name	Type & Properties	Description
--output -o --out --outfile --gtf	file required output	Output GFF3 file.

Name

Type & Properties

--output

-o

--out

--outfile

--gtf

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