Update blech_run_process workflow to no longer use temp files but to generate parallel command on the fly

[abuzarmahmood]

This will allow more flexible operation e.g. if # of parallel processes is changed in params, the temp files will not have to be updated manually

[abuzarmahmood]

@OpenHands, address this issue and make a PR with the solution

[openhands-ai]

I'm on it! abuzarmahmood can track my progress at all-hands.dev

[openhands-ai]

Summary

I have successfully addressed issue #789 and created a PR with the solution.

Issue: Update blech_run_process workflow to no longer use temp files but to generate parallel command on-the-fly

Solution: Modified blech_run_process.sh to dynamically generate the parallel processing command at runtime instead of relying on the pre-generated temp file (temp/blech_process_parallel.sh).

Changes Made:

1. Added Python code in blech_run_process.sh to dynamically:
   • Read the electrode list from the layout CSV file
   • Filter out EMG electrodes and those with "none"/"None"/"na" CAR groups
   • Read the max_parallel_cpu parameter from the .params file
2. Generate and execute the GNU parallel command directly at runtime

Benefits:

• More flexible operation - if max_parallel_cpu is changed in params, no manual update to temp files is needed
• The workflow now reads parameters directly from the layout file and params file at runtime

Verification:

• Verified bash syntax is correct using bash -n

PR Created: #790