agat/agat_convert_bed2gff
gene annotations
GFF conversion
Description
The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).
Inputs
Name | Type & Properties | Description |
|---|---|---|
--bed | file required | Input bed file that will be converted. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o --out --outfile --gff | file required output | Output GFF file. If no output file is specified, the output will be written to STDOUT. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--source | string | The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data] |
--primary_tag | string | The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene] |
--inflate_off | boolean_true | By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option. |
--inflate_type | string | Feature type (3rd column in gff) created when inflate parameter activated [default: exon]. |
--verbose | boolean_true | add verbosity |
--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 orignal 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 v0.3.1 \
-main-script target/nextflow/agat/agat_convert_bed2gff/main.nf \
-params-file params.yaml Relationships
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Current component
agat/agat_convert_bed2gffbiobox v0.3.1
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