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Add VCF input option to Vapor WDL #771

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mwalker174 merged 3 commits into main from mw_vapor_vcf

Feb 4, 2025

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mwalker174 commented Jan 21, 2025

Enables VCF inputs in addition to BED in the Vapor workflow.
Adds Vapor.wdl to Dockstore yaml.
New utility method SubsetVcfToSample for subsetting to a single sample from a String. This is nearly identical to SubsetVcfBySamplesList which takes a samples list file instead.
Deletes unnecessary prefix input since sample names usually suffice for file naming.

Tested successfully in Terra on 8 samples.

mwalker174 added 3 commits

January 21, 2025 11:07


          Add vcf input option to Vapor

98c87df

Remove branch from yaml

Update VaporBatch runtime attr and input templates


          Change vapor preprocessing warnings to errors

c984cfa


          Add SVLEN to bed

39c4898

epiercehoffman approved these changes

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epiercehoffman left a comment

All looking good

mwalker174 merged commit c91ae82 into main

9 checks passed

mwalker174 deleted the mw_vapor_vcf branch

February 4, 2025 15:01

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