illusional / python-cwlgen

Generation of CWL programmatically. Available types: CommandLineTool, Workflow and Requirements

python-cwlgen

Python-cwlgen is a python library for the generation of CWL programmatically. It supports the generation of CommandLineTool, Workflow and DockerRequirement. The library works for both Python 2.7.12+ and 3.6.0.

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Common Workflow Language

Common Workflow Language (CWL) is a language to describe workflows. The user guide gives a gentle explanation of what its goals are, but broadly:

1. Stop writing bash scripts for long complex jobs.
2. Take pipelines anywhere (portability).
3. Enforce reproducibility guidelines.

This python repository is a python wrapper for most of the classes (work in progress), allowing you to build the structure of the workflow in Python and have this module generate and export CWL for you.

Nb: This doesn't check the logic of Workflows or CommandLineTools for you.
CWLTool has a --validate mode that you can use.

Quick-start guide

You can install python-cwlgen through pip with the following command:

pip install cwlgen

How it works?

This repository contains a number of python classes that mirror the CWL specifications (Workflow| CommandLineTool). In essence, each class's initializer has all of the properties it expects, which may be another object. The classes include the relevant docstrings to give you context of classes and their properties.

The examples/ folder contains some simple examples, however in essence you simply initialize the class you're trying to build. An initializer for a class has all of the properties it expects which may be another object.

Creating a CommandLineTool

import cwlgen

tool_object = cwlgen.CommandLineTool(tool_id="echo-tool", base_command="echo", label=None, doc=None,
                 cwl_version="v1.0", stdin=None, stderr=None, stdout=None, path=None)
tool_object.inputs.append(
    cwlgen.CommandInputParameter("myParamId", param_type="string", label=None, secondary_files=None, param_format=None,
                 streamable=None, doc=None, input_binding=None, default=None)
)

# to get the dictionary representation:
dict_to_export = tool_object.get_dict()

# to get the string representation (YAML)
yaml_export = tool_object.export_string()

# print to console
tool_object.export()

# print to file
tool_object.export("echotool.cwl")

References

CWL is developed by an informal, multi-vendor working group consisting of organizations and individuals aiming to enable scientists to share data analysis workflows. The CWL project is on Github.

Known issues

• SchemaDefRequirement doesn't parse the types subfield into the specific types (InputRecordSchema | InputEnumSchema | InputArraySchema), but leaves them as a simple dictionary.