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.
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. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o --out | file required output | Path to the output GFF file that contains filtered features. |
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. |
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 v0.3.1 \
-main-script target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf \
-params-file params.yaml Relationships
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Current component
agat/agat_sp_filter_feature_from_kill_listbiobox v0.3.1
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