Firecloud failures because it is looking for nonexistent output parameters

mleventhalmleventhal Cambridge, MAMember, Broadie ✭✭

Hi,

Since the new release, I have been running into issues with an old method that I had developed. In the snapshot I am using, the outputs "pileup.normalPileupFileOut" and "varScan.variantFileOutIndel" do not exist in the WDL and are not specified. The tasks in which these outputs would theoretically be specified run with a "succeeded" status, as does the rest of the pipeline, and the requisite outputs are produced. However, the task ends in the "failed" status (as seen in the screenshot) because it claims that the specified outputs do not exist. This is frustrating because while I have the output files, the outputs do not get written as data model annotations such that subsequent tasks are unable to access the results. What can I do to fix this? Thank you!

-Matt Leventhal

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