umccrise: support presigned URL parsing #94
Merged
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Mainly adding functionality for parsing umccrise outputs (HRD/Sigs/QCsum) via presigned URLs.
read_tsvgz
uses agz
connection prior to attempting to read the TSVs, in the same vein as described in Handle presigned URLs of gzipped JSONs #74.glims_read
is a convenience function for parsing the Google LIMS via{googlesheets}
.workflows
table) is enough to grab LibraryID and SampleID for tumor and normal, except for those runs prior to 2023-04-07 (tumor SampleID is not available for those). We can instead use the LibraryID from the Google LIMS to map those and fill in the gaps.