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External AF SVID INFO key is String type #283

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merged 1 commit into from
Jan 14, 2022

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epiercehoffman
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Updates

Tweaks to AnnotateVcf workflow:

  • SVID INFO key from AnnotateExternalAF should be a String type, not Float. This was causing issues with Hail
    • There are two ModifyVcf tasks, one in AnnotateExternalAF and one in AnnotateExternalAFPerContig. It appears that only the one in the per-contig WDL is used, but I updated both because they aren't identical so I was wary of deleting the other
  • Output name of annotated VCF was {prefix}.annotated.vcf.vcf.gz; removed extra .vcf
  • Spacing

Testing

  • Validated all WDLs and JSONs with womtool
  • Tested AnnotateVcf and verified that the output VCF name had one .vcf and the header reflected that the SVID INFO key is of type String

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@mwalker174 mwalker174 left a comment

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Thank you, looks fine to me!

@epiercehoffman epiercehoffman merged commit aa6e2a0 into master Jan 14, 2022
@epiercehoffman epiercehoffman deleted the eph_external_af_header_string branch April 22, 2022 19:32
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