agat/agat_convert_sp_gff2gtf
Description
The script aims to convert any GTF/GFF file into a proper GTF file. Full
information about the format can be found here:
https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
version selected the script will filter out the features that are not
accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
pseudogene) will be converted into gene feature and every level2 feature
(e.g mRNA ncRNA) will be converted into transcript feature. Using the
"relax" option you will produce a GTF-like output keeping all original
feature types (3rd column). No modification will occur e.g. mRNA to
transcript.
To be fully GTF compliant all feature have a gene_id and a transcript_id
attribute. The gene_id is unique identifier for the genomic source of
the transcript, which is used to group transcripts into genes. The
transcript_id is a unique identifier for the predicted transcript, which
is used to group features into transcripts.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--gff -i | file required | Input GFF/GTF file that will be read |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o --out --outfile --gtf | file required output | Output GTF file. If no output file is specified, the output will be written to STDOUT. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--gtf_version | string | Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value from AGAT config file (relax for the default config). The script option has the higher priority. * relax: all feature types are accepted. * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr. * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine. * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon. * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR. * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon. * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron. |
--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.gtf"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/biobox.git \
-revision v0.2.0 \
-main-script target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf \
-params-file params.yaml Relationships
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