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Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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build in validation that there is only 1 tumor type per individual in qc report #34

Closed Kurt-Hetrick closed 10 months ago

Kurt-Hetrick commented 1 year ago

i have no idea what I should expect, but trying to iterate through a qc report and determining what to do when an individual has multiple tumor types is present is currently undefined. and depending what is desired, can be complex in generating a list of unique instances to process...so until this is better defined by pi, lab, proj man, etc. i think it is best now for to add a validation that there are no individuals in the qc report that have multiple tumor types present in them and if there is, exit out of the submission and notify submitter that this is not allowed. a qc report can only have one tumor type per individual.

Kurt-Hetrick commented 1 year ago

should probably do the same thing for normals as well.

Kurt-Hetrick commented 1 year ago

as it stands right now should add a validation that every tumor has a normal in the qc report.

Kurt-Hetrick commented 10 months ago

this should no longer be necessary when migrating to new sample input manifest