Upgrade CNV WDLs to 1.0 spec #6506
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samuelklee
approved these changes
Mar 18, 2020
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Thanks for doing this @mwalker174, just one minor comment regarding the dict in PreprocessIntervals. Otherwise looks good to me!
Not sure what issues are still open regarding taking advantage of additional functionality that WDL 1.0 provides (e.g., optional localization of BAMs), but perhaps it's worth filing and prioritizing them.
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| Int machine_mem_mb = select_first([mem_gb, 2]) * 1000 | ||
| Int command_mem_mb = machine_mem_mb - 500 | ||
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| # Determine output filename | ||
| String filename = select_first([intervals, "wgs.preprocessed"]) |
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Thanks for catching these!
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-Fixes broken input in somatic funcotator test
-Removes some unused resource variable defaults
-Adds
set -uin some tasks