The "store" command in CLI only works for file uploads but fails if there are nested subdirectories inside a directory.
Use Case #1:
I am trying to upload data for one of our collaborators from Aspera Transfer Server to Synapse. The main directory has numerous subdirectories and each subdirectory has many nested sub-subdirectories. Since we dont have direct linking of Aspera Server to Synapse, I am downloading the data into an AWS linux instance and then manually uploading to Synapse. For most subdirectories, I am uploading files using the "store" command from CLI. But for directories with many levels of nested sub-directories, the command fails and the only alternative is to go into python and use "SyncToSynapse". This is error prone and cumbersome since it requires generation of manifests, setting up of python environment, etc.
Use Case #2:
For Workflows, the command line version of recursive "store" will be important to ensure smooth transition from one step to another while saving output files/directories directly into synapse and help maintain provenance. This issue has been raised in the CLI Slack channel 3 months ago and seems to have been documented by KimYen. So maybe there is another open JIRA ticket about it