Description
The script provides exhaustive statistics of a gft/gff file.
If you have isoforms in your file, even if correct, some values calculated
might sounds incoherent: e.g. total length mRNA can be superior than the
genome size. Because all isoforms length is added... It is why by
default we always compute the statistics twice when there are isoforms,
once with the isoforms, once without (In that case we keep the longest
isoform per locus).
Type
bash_script
License
GPL-3.0
Keywords
Contributors
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 v0.4.2 \
-main-script target/nextflow/agat/agat_sp_statistics/main.nf \
-params-file params.yaml Name | Type & Properties |
|---|---|
--gff -i | file required |
--gs_fasta | file |
Name | Type & Properties |
|---|---|
--output -o | file required output |
Name | Type & Properties |
|---|---|
--plot -p -d | boolean_true |
--gs_size | integer |
--verbose -v | integer |
--config -c | file |