Apply some fixes to WDL examples #689
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These are fixes for some of the comments I left at #669
I'm merging into
wdl-1.1.3instead so the eventual merge intowdl-1.1by #669 will be cleaner.There are only two tests left that don't work:
hisat2andgatk_haplotype_caller. I haven't look at them yet as I don't have much experience with running the hisat2 or gatk pipeline.Other than those two, I believe the rest of the examples work.
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