> ## 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.

# Advanced: Flagged Runs & Output Routing

> Control whether flagged runs move into FLAGGED_* directories and whether final files are produced.

# Flagged Runs & Output Routing

Use a task‑level config switch to control how flagged runs write files and whether they propagate to final outputs.

## Current Behavior (default)

* `save_raw_to_set` / `save_epochs_to_set` write into directories named `FLAGGED_<stage>` when the run is flagged.
* During `_entrypoint`, post‑completion data is saved with `flagged` set to the task’s flagged status; final outputs are then skipped if the run is flagged.
* `copy_final_files` ignores any post‑completion directories whose names start with `FLAGGED`, so flagged runs never appear in the `final_files` folder.

## Make movement optional

Introduce a boolean task config `move_flagged_files` (default: `True`).

* When `True` (default): flagged runs are quarantined into `FLAGGED_*` directories and do not produce final files.
* When `False`: flagged runs keep normal directory names and still produce final files. The run remains “flagged” for your tracking, but routing is not altered.

### Configure in a task file

```python theme={null}
config = {
    # ... your existing settings ...
    "move_flagged_files": False,  # keep normal names and still produce final files
}
```

## Example outcomes

With `move_flagged_files: True` (default):

```text theme={null}
output/
  FLAGGED_raw_set/
  FLAGGED_epochs_set/
exports/
  (no files copied from flagged run)
```

With `move_flagged_files: False`:

```text theme={null}
output/
  raw_set/
  epochs_set/
exports/
  (files copied as usual)
```

## Recommendations

* Leave enabled for production QC to quarantine suspect outputs.
* Consider disabling temporarily during development or controlled analyses where you must collect outputs regardless of flags.

## Related

* See Advanced → Task Variables for defining additional task‑specific controls: `/advanced/task-variables`