Compi is an extremely simple application framework for portable computational pipelines. A computational pipeline can be seen as a set of processing steps that run one after one (or ocassionally in parallel if they are independent).

There are many fields where computational pipelines constitute the main architecture of applications, such as big data analysis or bioinformatics.

Many pipelines combine third party tools along with custom made processes, conforming the final pipeline. Compi is the framework helping you to create the final - and portable - application.

Pipeline Specification (XML)

Pipelines are specified in an XML file. The main purpose of this file is to define which atomic tasks your pipeline has, their dependencies (those tasks that need to be run before each task), and the parameters the user can specify and that will be used inside the tasks.

This file contains:

• <task> elements, which define your pipeline steps, their dependencies are defined with the after attribute. Inside the element, you place the code to be run when the task starts.
• <param> elments, which declare and describe the parameters of your pipeline. Inside any task you can use a parameter with ${parameter_name}.

<?xml version="1.0" encoding="UTF-8"?>
<pipeline xmlns="http://www.sing-group.org/compi/pipeline-1.0"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
    <version>1.0</version>
    <params>
        <param name="name" shortName="n">Your name</param>
        <param name="output" shortName="o">Output file</param>
    </params>
    <tasks>
        <task id="greetings" params="name output">
            echo "Hi ${name}" > ${output}
        </task>
        <task id="bye" after="greetings" params="name output" 
          interpreter="python3 -c &quot;${task_code}&quot;">
import os
name = os.environ['name']
output = os.environ['output']
f = open(output, "a")
f.write("bye " + name + "\n")
f.close()
        </task>
    </tasks>
</pipeline>