Fix data type and add options in picard

common-workflow-library / legacy

Deprecated

https://github.com/common-workflow-library/bio-cwl-tools

Apache License 2.0

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Fix data type and add options in picard #145

Closed jmchung closed 6 years ago

jmchung commented 6 years ago

This patch changes the data types for removeDuplicates and readSorted from boolean? to string?. If we pass the true to those ids, it just adding the prefixes to the command line and cause the exceptions. For example, we will get removeDuplicates= instead of removeDuplicates=true. This PR also add VALIDATION_STRINGENCY option in cwl to support stringency setting.

jmchung commented 6 years ago

cc @mr-c Can you help review this? Thanks.

mr-c commented 6 years ago

Hello @jmchung , this looks good -- thank you! I'll merge this for now, feel free to create another pull request if you want to use Enums for additional clarity.

jmchung commented 6 years ago

Thanks @mr-c :)