# QuNex commands and general usage overview

This page contains some basic information about how to use QuNex and access basic help for QuNex commands.

## QuNex commands

QuNex Suite features an extensive and growing list of commands, which accomplish various operations.

To get some basic information simply run 

``` bash
qunex
```

To get the comprehensive up-to-date list of all commands available in QuNex with short descriptions, run the following call from the terminal:

``` bash
qunex --a
```

To obtain further in-line documentation for a given command run:

``` bash
qunex <command_name> --h
```

When perusing documentation, please note the following conventions used:

* Square brackets `[]` denote a parameter that is optional. The value listed in the brackets is the default value used if the parameter is not explicitly specified.
* Angle brackets `<>` describe what value should be provided.
* Dashes or "flags" `-` in the documentation define input variables.
* Command names and parameters are either in small or "camel" case.
* Usage descriptions are in regular "sentence" case.
* Option values are usually specified in capital case (e.g. `YES`, `NONE`).

## Example

``` bash
qunex create_batch \
    --sessionsfolder="<path to sessions folder>" \
    [--overwrite="no"]
```

In the above example the user should provide the path to the folder with session data and optionally 
set the pipeline and overwrite parameters. The default value for the pipeline parameter is "hcp" while
the default value for the overwrite parameter is "no".

## General use syntax

QuNex commands are used through the `qunex` call. The general use form is:

``` bash
qunex <command_name> --parameter="<value>" --parameter="<value>" ...`
```

## QuNex versioning

QuNex follows the semantic versioning system: [https://semver.org/](https://semver.org/). Given a version number MAJOR.MINOR.PATCH:

* MAJOR version is increased when incompatible API changes are made,
* MINOR version is increased when functionality is added in a backwards-compatible manner, and
* PATCH version is increased when backwards-compatible bug fixes are introduced.

The version history and change log can be found in the `README.md` file within the QuNex repository: [https://gitlab.qunex.yale.edu/qunex/qunex](https://gitlab.qunex.yale.edu/qunex/qunex).

The QuNex version in the provided release is listed in the `VERSION.md` file or can be invoked via the command line by running:

``` bash
qunex –-version
```