agat/agat_sq_stat_basic
gene annotations
gff
statistics
Description
The script aims to provide basic statistics of a gtf/gff file.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--gff -i --file --input | file required multiple | Input GTF/GFF file. |
--genome_size -g | integer | That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide an INTEGER. Or you can also pass a fasta file using the argument --genome_size_fasta. If both are provided, only the value of --genome_size will be considered. |
--genome_size_fasta | file | That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide the genome in fasta format. Or you can also pass the size directly as an integer using the argument --genome_size. If you provide the fasta, the genome size will be calculated on the fly. If both are provided, only the value of --genome_size will be considered. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output file. The result is in tabulate format. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--inflate | boolean_true | Inflate the statistics taking into account feature with multi-parents. Indeed to avoid redundant information, some gff factorize identical features. e.g: one exon used in two different isoform will be defined only once, and will have multiple parent. By default the script count such feature only once. Using the inflate option allows to count the feature and its size as many time there are parents. |
--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.txt"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.4.0 \
-main-script target/nextflow/agat/agat_sq_stat_basic/main.nf \
-params-file params.yaml Relationships
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Current component
agat/agat_sq_stat_basicbiobox v0.4.0
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