Code Tool¶

Note

BETA: Available in v0.9.0 and later

A code tool is an abstract concept in Janis, that aims to execute arbitrary code inside a container.

Currently there is only one type of CodeTool:

janis.PythonTool

The aim is to make it simpler to perform basic steps within your container, for example say I want to perform some basic processing of a file that isn’t trivial in Janis (and hence CWL / WDL) but is in a programming language, Janis gives you the functionality to make this possible.

Creating a new code tool type¶

This process is designed to be fairly simple, but there are a few important notes:

Your tool must log ONLY a JSON string to stdout (this will get parsed later)
The prepared_script block must return a string that will get written to a file within the container to be executed that can accept inputs via command line. Within the PythonTool, you’ll see that a parser (by argparse) is generated in this method.

import janis_core as j

class LanguageTool(CodeTool):
    # You might leave these fields to be overriden by the user
    def inputs(self) -> List[TInput]:
        pass

    def outputs(self) -> List[TOutput]:
        pass

    def base_command(self):
        pass

    def script_name(self):
        pass

    def container(self):
        pass

    def prepared_script(self):
        pass

    def id(self) -> str:
        pass

    def version(self):
        pass