Setup resources
ENEO heavily depends on public genetic databases for germline probability estimation plus other fairly common resources daily needed for bioinformatics. In order to make the download and configuration of resources for the workflow as smooth as possible, a python configuration script is available inside setup/download_res.py. As the workflow depends on Ensembl annotation, downloading resources is not enough, as they may need a chromosome naming conversion: thus some common used tools like bcftools are required. To run the automatic setup, first create a conda environment using the setup_env.yml file located inside the setup folder.
Then activate the conda environment, and launch the configuration script as follows, specifying the right outfolder.
python3 download_res.py --config ../config/config_main.yaml --json resources.json --outfolder resources
What if I already got some of them?
The configuration script works by controlling the existence of the files whose path is written inside the main configuration file conf_main.yaml, located in the config folder. If any of those files are already in your machine, just edit the configuration file adding the right absolute path. The script will check for its presence without re-downloading it.
⚠️NOTE⚠️: As stated before, the annotation for all the files is the one provided by the Ensembl consortium. Files like the dbSNPs are often available with different chromosome naming: include them manually only if you're sure that the naming is right.