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wtsi-hgi / gatk-cwl-generator

Generates CWL files from the GATK documentation
MIT License
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CWL CommandLineTools such as HaplotypeCaller include `analysis_type` input #11

Closed jrandall closed 6 years ago

jrandall commented 6 years ago

There is an argument in the GATK json docs for CommandLineTool that specifies the --analysis_type (-T) which is the specific tool to invoke.

The current gatk-cwl-generator generates CWL for specific tools that inclues an input called analysis_type. This makes no sense - if invoking HaplotypeCaller using the HaplotypeCaller.cwl CommandLineTool, there should be no option for what value to use for -T - it should be fixed as HaplotypeCaller.

ThomasHickman commented 6 years ago

This is fixed in version 2.0