branches explained & current status of the pipeline

[eroesti]

Here there are some additional explanation regarding the last branches I created:

1. renv-optional: in this branch the library rent was deactivated (renv::deactivate). This was done due to the many problems performing the Jascap pipeline for the Jian/Ajith project. The following branches were created also based on the rent::deactivate mode.

2. Jian_no azimuth_annotation: Jian project contains mouse-data, thus the reference azimuth was not useful. Even though we left the other human annotations in, the azimuth was giving problem, thus, the command lines containing it were momentarily removed. In this branch, something went wrong, and can therefore be deleted! The correct branch without the azimuth reference is the below one: Jian_2.

3. Jian_2: the commands in this branch works without stopping until the pre-processing script. The next step is the pseudobulk scripts, and there are still some bugs to correct.
   This branch doesn't include renv() library, as mentioned above it was deactivated, and doesn't contain any azimuth reference.

Next steps are:

• fixing bugs from the pseudobulk R script
• adding reports to pipeline