agat/agat_sp_merge_annotations
gene annotations
merge
gff
Description
Merge different gff annotation files into one. It uses the AGAT parser that takes care of
duplicated names and fixes other oddities met in those files.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--gff -f | file required multiple | Input GTF/GFF file(s). |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o --out | file required output | Output gff3 file where the gene incriminated will be writen. |
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). |
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 v0.3.0 \
-main-script target/nextflow/agat/agat_sp_merge_annotations/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
agat/agat_sp_merge_annotationsbiobox v0.3.0
Uses
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No component dependencies found.