Managing multiple projects

There two different option of how to manage the data and software if you want to run the ARMOR workflow on more than one project:

1. Keep the ARMOR repository and the data of each project together in a single directory: This way, the software (the Snakefile, the scripts, the Rmd files and the config.yaml) and data from each project are contained in a single directory. The configuration of the workflow will be preserved and thus, it will be very easy to reproduce results. However, you will have ARMOR in multiple physical locations, which means the installed software might be duplicated if you are using conda environments.
2. Clone the ARMOR repository only once, keep the data in a separate directory: This way, the ARMOR directory can be reused for many different projects. This might be useful if you have space or time constraints, i.e. the conda environments will be created only once and you can reuse them for many project. The configuration is a bit more complicated, because you will need a different config.yaml file for each project (you can have them all located in the ARMOR directory or one in each project directory.) You will have to specify the Snakefile and the config.yaml file everytime you want to run the workflow. See Running the analysis for more details.