Sophios documentation

Sophios is a high-level way to create, build, and execute Common Workflow Language (CWL) workflows. It is for people who already have useful command-line tools and want to turn them into portable, inspectable workflows without making raw CWL the day-to-day authoring language.

With Sophios, you describe command-line tool contracts, compose those tools into workflow graphs, compile the graph to CWL, and run the result locally or prepare it for execution on remote, HPC, or cloud resources. The generated workflow, generated job inputs, exported .wic source, and execution artifacts remain available for inspection.

The practical outcome is straightforward: workflow authors work in Python by default, execution remains grounded in standard CWL, and teams can inspect the exact artifacts that a local runner or remote execution service will receive.

There are two authoring modes:

  • the Python Workflow API, which is the primary interface for most users and application code;

  • the .wic YAML DSL, which is the file-native interface for standalone, headless, auditable, and advanced compiler-oriented workflows.

Why Sophios?

Most scientific and data workflows begin as command-line tools plus a shell script. That is a good starting point, but it becomes hard to maintain when the workflow needs explicit tool contracts, portable execution, validated inputs, generated artifacts, reproducible local runs, or execution on external resources. Sophios gives that work a clear structure:

  • a CommandLineTool captures what one tool expects and produces,

  • a Step places that tool inside a workflow,

  • a Workflow owns the graph and named outputs,

  • compilation emits CWL and job inputs you can inspect,

  • submission-oriented helpers validate payloads before remote execution.

The goal is not to hide the workflow. The goal is to make the workflow easier to author while keeping the compiled CWL and execution artifacts concrete enough to understand, debug, and review.

Start Here

Python API

Advanced YAML and Operations

Developers

Indices and tables