janis-patterns

This is a place for documenting common patterns that you might want to achieve using Janis. This repository is work-in-progress. Please raise an issue if there are patterns you think would be valuable in this repository.

Contents

Quick debugging tip

The quickest way to verify whether your janis workflow / command tool is connected correctly, is to translate it to CWL or WDL. There are two quick ways to do that:

We usually recommend WDL to verify, as it's intuitive to compare the command line and connections.

1. Add the following block of code to your python file, then run the file:

   if __name__ == "__main__":
       YourWorkflowOrTool().translate(
           "wdl", to_console=True
       )

2. OR, translate using the command line:

   $ janis translate yourpythonfile.py wdl # or cwl

Declaring types

• Janis types
• Python Types (types/pythontypes.py)

Command line declaration

Regular

• Positional arguments

• Arguments with a prefix

• Array arguments:

  • Separator

Advanced

• Joining multiple commmands together

Scatter execution

The scatter folder

• Regular scatter (by a single field).
• Scatter by multiple fields:
  • Dot Product - For each corresponding entries in the inputs (must have the same length).
  • Cross product - For every combination of items (distributive).

Workflow vs Workflow Builder