> ## Documentation Index
> Fetch the complete documentation index at: https://docs.autocleaneeg.org/llms.txt
> Use this file to discover all available pages before exploring further.

# Running an AutocleanEEG Pipeline

> Configure a workspace, select a task, and run reproducible EEG preprocessing with clear quality-control (QC) outputs.

<Steps>
  <Step title="Prerequisites">
    * AutocleanEEG Pipeline (see [Installation](http://localhost:3000/installation))
    * Download our Resting EEG example dataset from [Zenodo](https://zenodo.org/records/17042258)
  </Step>

  <Step title="Check Workspace Location">
    By default, AutocleanEEG Pipeline creates a workspace folder named **`Autoclean-EEG`** inside your **Documents** folder.

    * Verify the workspace location:

    ```bash theme={null}
    % autocleaneeg-pipeline workspace show

          AutocleanEEG Pipeline Workspace                                             
              Current configuration                                      

      ✓ Workspace ~/Documents/Autoclean-EEG                              
              💾 Free space 472.9 GB                                      

    ```

    <Tip>
      To open the workspace in your file explorer try:

      `autocleaneeg-pipeline workspace explore`
    </Tip>
  </Step>

  <Step title="List Tasks">
    List available tasks in your workspace:

    ```bash theme={null}
    autocleaneeg-pipeline task list
    ```

    <img src="https://mintcdn.com/cincibrainlab/6cpQKO2fi2WXdMQG/images/first-pipeline-task-list.png?fit=max&auto=format&n=6cpQKO2fi2WXdMQG&q=85&s=49559d7085f98f96b8615be6ce156978" alt="AutocleanEEG task list showing built-in and custom tasks" style={{ borderRadius: '0.5rem', marginTop: '0.75rem' }} width="1990" height="705" data-path="images/first-pipeline-task-list.png" />

    <Tip>
      Task creation can be entirely custom and complex, incorporating Python, R, or MATLAB code. For this guide, we're using a simple built-in task to get you started quickly.
    </Tip>
  </Step>

  <Step title="Copy Task">
    Copy the built-in `RestingState_Basic` task and rename it for our tutorial:

    ```bash theme={null}
    autocleaneeg-pipeline task copy RestingState_Basic RestingState_Tutorial
    ```

    This creates a custom copy that you can modify without affecting the original built-in task.
  </Step>

  <Step title="Set Active Task">
    Set the copied task as your active task:

    ```bash theme={null}
    autocleaneeg-pipeline task set
    ```

    Select the number corresponding to `RestingState_Tutorial` from the displayed list.
  </Step>

  <Step title="Set Input File">
    Set the input EEG file for processing:

    ```bash theme={null}
    autocleaneeg-pipeline input set
    ```

    Copy and paste the full path to your downloaded example file when prompted.

    <Tip>
      You can also set a folder path for batch processing multiple files at once.
    </Tip>
  </Step>

  <Step title="Confirm Configuration">
    Verify that workspace, task, and input are all properly configured:

    ```bash theme={null}
    autocleaneeg-pipeline
    ```

    This displays your current pipeline configuration and confirms everything is set correctly.
  </Step>

  <Step title="Run Pipeline">
    Start the processing pipeline:

    ```bash theme={null}
    autocleaneeg-pipeline process
    ```

    Confirm the details when prompted and type `yes` to start the pipeline running.
  </Step>

  <Step title="View Outputs">
    When processing is complete, explore the generated outputs:

    ```bash theme={null}
    autocleaneeg-pipeline workspace explore
    ```

    This opens your workspace folder to view the processed results and quality control outputs.

    <Note>
      The next sections go over outputs in detail, including BIDS compliance, subject reports, processing logs, and intermediate pipeline steps.
    </Note>
  </Step>
</Steps>