# QuNex 'turnkey' workflow and 'batch' engine

The QuNex Suite enables 'Turnkey' processing across the supported functions. This feature enables full automation across selected QuNex steps. This is accomplished via the [`run_turnkey`](../../api/gmri/run_turnkey.rst) QuNex command that enables one step processing of sessions.

It is less flexible than running individual `qunex` commands; however, it offers the ability to run the entire QuNex Suite workflow in a single command, either locally or via XNAT.

The QuNex turnkey workflow can be invoked in two ways, which can be specified via the following flag:

`--turnkeytype=<turnkey_run_type>`

The two turnkey workflow options are `local` or `xnat`, which will differ in their parameter specification.

````{note}
The command examples below do not provide the exhaustive list of all `run_turnkey` parameters. To get a full parameter listing consult [`run_turnkey`](../../api/gmri/run_turnkey.rst) command reference or invoke help via `qunex run_turnkey`.
````

## QuNex run_turnkey on a cluster or local workstation

## Data assumptions

The raw data folder should be:

```sh
${RAW_DATA}
        ├── HCPA001.zip
        ├── hcp_mapping.txt
        └── parameters.txt
```

The folder needs to contain the individual session data (dicom, bids, compressed format). If the data is compressed, it is expected to hold a single session and be named using the following specification:

`<subject id>_<session id>.zip`.

For example, in the case below this would be `HCPA001.zip`.

In addition, the folder needs to contain the two QuNex settings files:

* [parameters.txt](../Overview/file_batch_txt)
* [hcp_mapping.txt](../Overview/file_mapping)

## The run_turnkey command specification

The processing from data ingestion to creation of processing results is then completed by running the following example command, which specifies how to run the turnkey workflow for a **local workstation**:

```sh
# - Folder name to generate
STUDY_NAME="QUNEX_UseCase"

# - Master Working Directory
WORK_DIR="/gpfs/project/fas/n3/Studies"

# - Location for Raw Data
RAW_DATA="/gpfs/project/fas/n3/software/qunexdata/QUNEXTurnkeyUseCase"

# - Name of session to process
SESSIONS_LIST="HCPA001"

# - Input files
INPUT_BATCH_FILE="${RAW_DATA}/parameters.txt"
INPUT_MAPPING_FILE="${RAW_DATA}/hcp_mapping.txt"

# - Type of QuNex Turnkey run
RUNTURNKEY_TYPE="local"

# - QuNex Turnkey steps
RUNTURNKEY_STEPS=\
"create_study,map_raw_data,create_session_info,setup_hcp,create_batch,hcp_pre_freesurfer,hcp_freesurfer,hcp_post_freesurfer,run_qc_t1w,hcp_fmri_volume,hcp_fmri_surface,run_qc_bold,map_hcp_data,create_bold_brain_masks,compute_bold_stats,create_stats_report,extract_nuisance_signal,preprocess_bold,compute_bold_fc_seed,compute_bold_fc_gbc"

# - Command call
qunex run_turnkey \
    --rawdatainput="${RAW_DATA}" \
    --dataformat="DICOM" \
    --paramfile="${INPUT_BATCH_FILE}" \
    --mappingfile="${INPUT_MAPPING_FILE}" \
    --workingdir="${WORK_DIR}" \
    --projectname="${STUDY_NAME}" \
    --path="${WORK_DIR}/${STUDY_NAME}" \
    --sessions="${SESSIONS_LIST}" \
    --turnkeytype="${RUNTURNKEY_TYPE}" \
    --bolds="all" \
    --runparcellations=all \
    --turnkeysteps="${RUNTURNKEY_STEPS}" \
    --overwritestep="no"
```

The command will generate `QUNEX_UseCase` study folder where all the results will be present at the end.