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broadinstitute / wdltool

BSD 3-Clause "New" or "Revised" License
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issue with wdltool 0.4? #12

Closed eddiebroad closed 6 years ago

eddiebroad commented 8 years ago

I try to use wdltool validate on a WDL and it seems to not catch an error in the WDL.

In the example "bad" WDL attached the call to VCF_to_MAF_task has the line "inputVCF=inputVCF" but the "inputVCF" exists only in the task but not at the workflow level but invoking wdltool 0.4 on it seems to NOT cause an error. Shouldn't it be saying the WDL has an error because inputVCF does not exist at the workflow level?

I downloaded the wdltool from the latest release https://github.com/broadinstitute/wdltool/releases/download/0.4/wdltool-0.4.jar

the two WDLs are attached. wdl_files.zip

wm8b1-75c:red_bug esalinas$ find *.wdl -exec java -jar wdltool-0.4.jar validate  {} \;

wm8b1-75c:red_bug esalinas$ diff  good.wdl  bad.wdl 
188c188
<           inputVCF=inVCF,

---
>           inputVCF=inputVCF,
wm8b1-75c:red_bug esalinas$
mcovarr commented 6 years ago

Issue moved to broadinstitute/cromwell #2876 via ZenHub