agat/agat_sq_stat_basic

gene annotations

gff

statistics

Description

The script aims to provide basic statistics of a gtf/gff file.

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

gff

statistics

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.txt"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/agat/agat_sq_stat_basic/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--gff -i --file --input	file required multiple	Input GTF/GFF file.
--genome_size -g	integer	That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide an INTEGER. Or you can also pass a fasta file using the argument --genome_size_fasta. If both are provided, only the value of --genome_size will be considered.
--genome_size_fasta	file	That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide the genome in fasta format. Or you can also pass the size directly as an integer using the argument --genome_size. If you provide the fasta, the genome size will be calculated on the fly. If both are provided, only the value of --genome_size will be considered.

Name

Type & Properties

--gff

-i

--file

--input

file

required

multiple

--genome_size

-g

integer

--genome_size_fasta

file

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output file. The result is in tabulate format.

Name

Type & Properties

--output

-o

file

required

output

Arguments

Name	Type & Properties	Description
--inflate	boolean_true	Inflate the statistics taking into account feature with multi-parents. Indeed to avoid redundant information, some gff factorize identical features. e.g: one exon used in two different isoform will be defined only once, and will have multiple parent. By default the script count such feature only once. Using the inflate option allows to count the feature and its size as many time there are parents.
--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

--inflate

boolean_true

--config

-c

file