agat/agat_convert_bed2gff

gene annotations

GFF conversion

Description

The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).

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 v0.3.1 \  
  -main-script target/nextflow/agat/agat_convert_bed2gff/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--bed	file required	Input bed file that will be converted.

Name

Type & Properties

--bed

file

required

Outputs

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

Name

Type & Properties

--output

-o

--out

--outfile

--gff

file

required

output

Arguments

Name	Type & Properties	Description
--source	string	The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]
--primary_tag	string	The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]
--inflate_off	boolean_true	By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.
--inflate_type	string	Feature type (3rd column in gff) created when inflate parameter activated [default: exon].
--verbose	boolean_true	add verbosity
--config -c	file	Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal 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

--source

string

--primary_tag

string

--inflate_off

boolean_true

--inflate_type

string

--verbose

boolean_true

--config

-c

file