[IBCDPE-587] adds bash script for syncing LENS reference files

[BWMac]

This PR adds a bash script that can be used for reproducibly sync-ing the LENS Nextflow Workflow reference files to our sage-igenomes S3 bucket. The files and their structure within the subdirectories can be viewed here.

I followed the example provided by Bruno as much as I could, but there are a couple of differences.

1. There is no all-encompassing location where these reference files are stored. Instead, the LENS devs provide 3 bash scripts that are used to generate the reference files from different locations. These scripts are downloaded and executed in this script.
2. The file structure is different in that there are both files and folders present in the prefix directories used in this script, so I decided against sync-ing with longer prefixes as Bruno did in the example for simplicity.

I considered not including prefixes and the sync loop at all because I am not 100% certain that the prefixes won't change in the future.

After a follow-up discussion with iAtlas stakeholders, we elected to look closer at the reference file-downloading bash scripts used to set up the reference directory. I have made some updates to these scripts and included them in this PR. before running these scripts, it is assumed that you have followed the setup instructions provided by the LENS team here and that the raft directory has been created.

Documentation of the other additional steps I needed in order to run these scripts is also a WIP.

NOTE: The generate_mouse_references.sh script is still a WIP, owing to the fact that the starfusion section needs to be updated. As a result, I have commented out the download_mouse_references.sh executing lines.

[BWMac]

I made another small commit to this branch but the PR does not seem to be updating for some reason...

[thomasyu888]

I know this is a draft, but some prelim comments.

[thomasyu888]

🛠️ this looks great! Thanks!