agat/agat_convert_mfannot2gff
gene annotations
GFF
Mfannot
Description
Conversion utility for MFannot "masterfile" annotation produced by the
MFannot pipeline. Reports
GFF3 format.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--mfannot -m -i | file required | The mfannot input file. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--gff -g -o | file required output | The GFF output file. |
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'
gff: "$id.$key.gff.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_convert_mfannot2gff/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
agat/agat_convert_mfannot2gffbiobox v0.3.0
Uses
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