Fix or remove remove contam TSV parsing

aofarrel / clockwork-wdl

WDLization of clockwork

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Fix or remove remove contam TSV parsing #39

Open aofarrel opened 2 months ago

aofarrel commented 2 months ago

The TSV spit out by the decontam task is different based on the decontamination reference genome that gets used. Currently, when the CRyPTIC reference is used, the wrong thing happens.

aofarrel commented 2 months ago

That ain't right! https://github.com/aofarrel/clockwork-wdl/blob/35f69ca4bfeb981d63f01f7c472eaf17abe292d2/tasks/combined_decontamination.wdl#L624C21-L624C28