Configuration

Edit or create your config.yaml file in the workflow folder. This file contains all the parameters for the pipeline, including paths to your raw data, processed data, and Suite2p options. Here is an example of a config.yaml file:

raw_data_base: "/path/to/raw/"
processed_data_base: "/path/to/processed/"

suite2p_ops:
  fs: 7.5
  nplanes: 1
  tau: 0.8
  nonrigid: true
  diameter: 10

slurm:
  use_slurm: true
  partition: "cpu"
  mem_mb: 16000
  cpu_per_task: 1
  tasks: 1
  nodes: 1

If you don’t have access to a cluster or SLURM, set use_slurm: false to run locally.