Fix reading sequences of steps/etc.

Barski-lab / cwl-airflow

Python package to extend Airflow functionality with CWL1.1 support

https://barski-lab.github.io/cwl-airflow

Apache License 2.0

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Fix reading sequences of steps/etc. #34

Closed mruffalo closed 4 years ago

mruffalo commented 4 years ago

The CWL spec allows many things to be stored as key/value mappings, or as sequences with each value being a mapping that includes a id key. Add support for workflow steps which are stored as sequences by introducing a get_items function that returns key/value pairs for both sequences and mappings.

michael-kotliar commented 4 years ago

Hi! Thank you for your PR. Could you please provide an example workflow that you used to test this PR.

mruffalo commented 4 years ago

Gladly: https://github.com/hubmapconsortium/salmon-rnaseq/blob/master/pipeline.cwl