# MSK-ACCESS command-line tools

* Free software: Apache Software License 2.0
* Documentation: <https://msk-access.gitbook.io/command-line-tools-cwl/>

## Features

Create command line tools in common workflow language to generate workflows.

## Installation

Clone the repository:

```
git clone --depth 50 https://github.com/msk-access/cwl-commandlinetools.git
```

**Follow the README in repsective tool folder for execution of the tool.**

## Credits

This package was created with Cookiecutter *and the `audreyr/cookiecutter-pypackage`* project template.

* Cookiecutter: <https://github.com/audreyr/cookiecutter>
* `audreyr/cookiecutter-pypackage`: <https://github.com/audreyr/cookiecutter-pypackage>


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://cmo-ci.gitbook.io/command-line-tools-cwl/readme.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.
