agat/agat_sp_filter_feature_from_kill_list

gene annotations

filtering

gff

Description

Remove features based on a kill list. The default behaviour is to look at the features's ID.
If the feature has an ID (case insensitive) listed among the kill list it will be removed.
Removing a level1 or level2 feature will automatically remove all linked subfeatures, and
removing all children of a feature will automatically remove this feature too.

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

filtering

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"  
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_filter_feature_from_kill_list/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--gff -f --ref --reffile	file required	Input GFF3 file that will be read.
--kill_list --kl	file required	Text file containing the kill list. One value per line.

Name

Type & Properties

--gff

-f

--ref

--reffile

file

required

--kill_list

--kl

file

required

Outputs

Name	Type & Properties	Description
--output -o --out	file required output	Path to the output GFF file that contains filtered features.

Name

Type & Properties

--output

-o

--out

file

required

output

Arguments

Name	Type & Properties	Description
--type -p -l	string multiple	Primary tag option, case insensitive, list. Allow to specify the feature types that will be handled. You can specify a specific feature by giving its primary tag name (column 3) as: * cds * Gene * mRNA You can specify directly all the feature of a particular level: * level2=mRNA,ncRNA,tRNA,etc * level3=CDS,exon,UTR,etc. By default all features are taken into account. Fill the option with the value "all" will have the same behaviour.
--attribute -a	string	Attribute tag to specify the attribute to analyse. Case sensitive. Default: ID
--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).
--verbose -v	boolean_true	Verbose option for debugging purpose.

Name

Type & Properties

--type

-p

-l

string

multiple

--attribute

-a

string

--config

-c

file

--verbose

-v

boolean_true