feat: add defense-finder subworkflow

[matinnuhamunada]

Hi @ChMaWh, here is the first draft of defense-finder subworkflow:

Usage:

1. Create a conda environment and install the BGCFlow python wrapper :

# create and activate a new conda environment
conda create -n bgcflow -c conda-forge python=3.11 pip openjdk -y
conda activate bgcflow

# install `BGCFlow` wrapper
pip install git+https://github.com/NBChub/bgcflow_wrapper.git

# make sure to use bgcflow_wrapper version >= 0.2.7
bgcflow --version

2. Deploy BGCFlow, change your_bgcflow_directory variable accordingly:

# Deploy and run BGCFlow
bgcflow clone <your_bgcflow_directory> # clone `BGCFlow` to your_bgcflow_directory
cd <your_bgcflow_directory> # move to BGCFLOW_PATH
bgcflow init # initiate `BGCFlow` config and examples from template

3. Checkout to defense-finder branch:

git checkout defense-finder
bgcflow run --workflow workflow/defense-finder -n

4. To run it, remove the -n flag, and maybe define the number or cores to use:

bgcflow run --workflow workflow/defense-finder -c 8 #adjust the number of cores to use

5. Right now, the output is still located in data/interim/defense-finder

6. Modify your sample file in the config folder