What's Changed
* Update docs by CChahrour in https://github.com/alsmith151/SeqNado/pull/230
* Add ecoli to preset genomes by CChahrour in https://github.com/alsmith151/SeqNado/pull/229
* Add seqnado version to config by CChahrour in https://github.com/alsmith151/SeqNado/pull/229
* Fix typo in protocol.txt by CChahrour in https://github.com/alsmith151/SeqNado/pull/229
* Feat-dynamic slurm_partition by CChahrour in https://github.com/alsmith151/SeqNado/pull/229
* Refactor initialization process and add genome configuration by alsmith151 in https://github.com/alsmith151/SeqNado/pull/229
This commit refactors the initialization process in the `cli.py` file to include a new `init` command. The `init` command initializes the seqnado pipeline and sets up the correct environmental variables. It also adds the functionality to initialize genome files using a template file. The `get_genomes` function in the `helpers.py` file is modified to read the genome configuration from a JSON file and return the genome values. The commit also includes the addition of a new `init.sh` script that is used to initialize the environment for the SeqNado project. Lastly, a template file `genomes_template.json` is added to the `workflow/config` directory.
---------
Co-authored-by: CChahrour <catherine.chahrourgmail.com>
* Add init cli
* Add seqnado-init to tests
---------
Co-authored-by: alsmith <asmith151outlook.com>
Co-authored-by: Alastair Smith <49727900+alsmith151users.noreply.github.com>
**Full Changelog**: https://github.com/alsmith151/SeqNado/compare/v0.6.1...v0.6.2