I've currently been trying to run GenomeSTRiP CnvDiscoveryPipeline on Terra. I'm trying to find the correct sequence of workflows to go through. I couldn't match the wdl scripts on Firecloud with the stages described in this link.
My case is to run germline CNV discovery on a set of ~30 WGS (30X) samples with Mendelian diseases. I checked the RunCNVPipeline script and it seems like the most likely match for what I need. Do I need to run SingleStepPreprocessing/ before I run RunCNVPipeline? And Do I need to run CreatCnvCallset afterward, or is this a separate version of the CNVPipeline script? I hope to gain some guidance on the sequence of steps I need to run through on Terra.
It would be great if there is some sort of schematics describing the relations between each module. Thank you in advance!
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