agat/agat_convert_embl2gff
gene annotations
GFF conversion
Description
The script takes an EMBL file as input, and will translate it in gff format.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--embl | file required | Input EMBL file that will be read. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o --out --outfile --gff | file output | Output GFF file. If no output file is specified, the output will be written to STDOUT. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--emblmygff3 | boolean_true | Means that the EMBL flat file comes from the EMBLmyGFF3 software. This is an EMBL format dedicated for submission and contains particularity to deal with. This parameter is needed to get a proper sequence id in the GFF3 from an embl made with EMBLmyGFF3. |
--primary_tag --pt -t | string multiple | List of "primary tag". Useful to discard or keep specific features. Multiple tags must be comma-separated. |
--discard -d | boolean_true | Means that primary tags provided by the option "primary_tag" will be discarded. |
--keep -k | boolean_true | Means that only primary tags provided by the option "primary_tag" will be kept. |
--config -c | file | Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". 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 v0.4.2 \
-main-script target/nextflow/agat/agat_convert_embl2gff/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
agat/agat_convert_embl2gffbiobox v0.4.2
Uses
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