Python-CWLGen (Deprecated)

Warning

python-cwlgen is now deprecated, please use cwl-utils >= 0.4.

Example migration:

from cwl_utils import parser_v1_0

# You could alias this as cwlgen to simplify the migration
from cwl_utils import parser_v1_0 as cwlgen

Migration notes:

  • Method changes

    • get_dict() → save()
    • parse_cwl(cwlfile) → load_document(cwlfile)
    • parse_dict → No super clear analogue, but loaded through _RecordLoader(CommandLineTool) || _UnionLoader((CommandLineToolLoader, ...workflow + other loaders)

  • Field names:

    • Uses camelCase instead of snake_case
    • No more special field names, eg: - tool_id | workflow_id | input_id | etc → id - StepInput: inputs → in_

  • Other notes:

    • Classes aren’t nested anymore, ie: cwlgen.InitialWorkDirRequirement.Dirent → cwlutils.

    • Take care if you’re migrating to a newer spec, as some classes might have changed names (notably: InputParameter -> WorkflowInputParameter)

    • Don’t forget to catch all references of cwlgen, as missing one (or using mismatch versions of the parser) will cause:

      raise RepresenterError('cannot represent an object: %s' % (data,))
ruamel.yaml.representer.RepresenterError: cannot represent an object:
<cwlgen.common.CommandInputArraySchema object at 0x1100a5780>

If you have issues with the migration, please see this thread or raise an issue on CWLUtils.

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Python-cwlgen is a python library for the programmatic generation of CWL v1.0. It supports the generation of CommandLineTool and Workflows.

The library works for both Python 2.7.12+ and 3.6.0+.

Quick-start

You can install Python-CWLGen through pip with the following command:

pip install cwlgen

The classes very closely (if not exactly) mirror the CWL v1.0 specification. You can find more about their parameters in the following specifications: