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williamrowell
commented
Apr 23, 2024
williamrowell
commented
- tabs -> spaces
- populate meta and parameter_meta
- standardize input and output names
- flatten inputs and outputs by removing IndexData objects
- refactor many HiFi-human-WGS-WDL tasks into wdl-common tasks
- add gpu support for DeepVariant call_variants
- add stats outputs to many tasks
- ReferenceData struct replaced by ref_map_file, simplifying inputs
- Tertiary Analysis related inputs replaced by tertary_map_file, simplifying inputs
- high level statistics directly exposed from many tasks
- many tool versions updated
- singleton, for analyzing single samples; flat input and output structure for better compatibility with platforms like Terra - family, for analyzing families of related samples; still requires a more nested structure for inputs, and outputs are either arrays (for sample-level output) or flat (for joint/tertiary output)
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