> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/analysis/integrations/cwl-tool.md).

# CWL Tool

Common Workflow Language (CWL) provides an alternative workflow specification to WDL. This guide demonstrates running the `02_download_collection_files` workflow in CWL format using CWLtool and Docker.

### Prerequisites

* Python 3.6 or higher
* [Docker](https://docs.docker.com/desktop/)
* Optional: cURL and git

## Setup Instructions

You'll need to download:

* [cwltool](https://github.com/common-workflow-language/cwltool)
* [02\_download\_collection\_files.wdl](https://raw.githubusercontent.com/DNAstack/dnastack-client-library-worked-examples/master/examples/wdl/02_download_collection_files.wdl)

### Getting the Example Workflow

Download the worked examples repository using either method:

#### Clone with Git

```shell
git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git
```

Or [Download](https://github.com/DNAstack/dnastack-client-library-worked-examples/archive/refs/heads/master.zip) and Unzip

It is assumed that all commands will be run from the root directory of this repository on your local machine. From the directory where you’ve downloaded the examples repository.

```
cd dnastack-client-library-worked-examples/
```

### Installing CWL Tool

Install cwltool using either method:

Download and install [cwltool](https://github.com/common-workflow-language/cwltool) by one of the following methods.

#### Using `apt` for Debian, Ubuntu, and similar Linux distributions

```shell
sudo apt-get install cwltool
```

#### Or use `pip`

```shell
pip3 install cwlref-runner cwltool
```

## Running the workflow

To run the workflow:

```shell
cwltool ./examples/cwl/02_download_collection_files.cwl
```

Output files can be found in the current directory.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

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

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://docs.omics.ai/products/analysis/integrations/cwl-tool.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

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.