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wtsi-hgi / gatk-cwl-generator

Generates CWL files from the GATK documentation
MIT License
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Move reference_sequence, refIndex and refDict to the same folder initially #10

Closed ThomasHickman closed 6 years ago

ThomasHickman commented 6 years ago

If you run this tool with the path specified for reference_sequence, refIndex or refDict in different folders, this will fail to run. It would be nice if reference_sequence, refIndex or refDict were moved to the same directory, before running HaplotypeCaller.

ThomasHickman commented 6 years ago

This could be achieved by using InitialWorkDirRequirement to populate a folder like ~/reference, where ~ is the working directory with the reference files

ThomasHickman commented 6 years ago

This should be sorted by having a workflow step that outputs the index and dict into secondaryFiles as a step before a gatk step