diff --git a/README.md b/README.md index bd40e20b..34d77153 100644 --- a/README.md +++ b/README.md @@ -166,6 +166,26 @@ The project uses GitHub Actions for automated testing on pull requests: - blech_clust_pre.sh : Runs steps 2-5 - blech_clust_post.sh : Runs steps 7-14 +### blech_autosort.sh Script + +The `blech_autosort.sh` script is designed to automate the process of clustering and post-processing electrophysiology data. It ensures that the necessary parameters are set correctly and executes the pre-processing, clustering, and post-processing steps in sequence. + +**Usage:** +```bash +bash blech_autosort.sh [--force] +``` + +- ``: Path to the directory containing the raw data files. +- `--force`: Optional flag to force re-processing even if previous results exist. + +**Functionality:** +- Checks for the existence of required parameter files and verifies that specific settings are enabled. +- Executes the `blech_clust_pre.sh` script to perform initial processing. +- Runs `blech_post_process.py` to add sorted units to the HDF5 file. +- Completes the workflow with `blech_clust_post.sh` for further processing. + +Ensure that the parameter files `sorting_params_template.json` and `waveform_classifier_params.json` are correctly configured before running this script. + ### Operations Workflow Visual ![nomnoml](https://github.com/user-attachments/assets/5a30d8f3-3653-4ce7-ae68-0623e3885210)