INSTALL.md

Installing a CWL Runner

To run CWL workflows, you'll need to install a CWL runner. The most popular CWL runner is cwltool, which is a reference implementation of the CWL standard. cwltool can be installed using pip, the Python package installer.

Here's how to install cwltool:

1. Install Python: cwltool requires Python 3.5 or later. If you don't have Python installed, you can download it from the official website: https://www.python.org/downloads/
2. Install pip: pip is the package installer for Python. If you don't have pip installed, you can download it from the official website: https://pip.pypa.io/en/stable/installing/
3. Install cwltool: Once you have pip installed, you can install cwltool using the following command:

pip install cwltool

4. Verify the installation: To verify that cwltool was installed correctly, you can run the following command:

cwltool --version

This should print the version number of cwltool.

YAML Syntax

CWL documents are typically written in YAML, which is a human-readable data serialization language. YAML files consist of a series of key-value pairs, with indentation used to indicate the hierarchy of the data.

Here's an example of a simple YAML file:

name: John Doe
age: 30
occupation: Software Developer

In this example, name, age, and occupation are keys, and John Doe, 30, and Software Developer are values.

Here are some important YAML syntax rules to keep in mind:

• YAML is case-sensitive
• YAML uses indentation to indicate hierarchy
• Indentation must be consistent throughout the file
• Lists are indicated using a dash (-) followed by a space
• Strings can be enclosed in single or double quotes

Here's an example of a YAML file that includes a list:

fruits:
  - apple
  - banana
  - orange

In this example, fruits is a key, and apple, banana, and orange are values in a list.

Familiarizing yourself with YAML syntax is essential for working with CWL documents, as CWL workflows and tools are typically defined using YAML.