Adding NIO and updating to WDL 1.0 to MT pipeline #6074
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ldgauthier
approved these changes
Aug 5, 2019
| File input_bam | ||
| String basename = basename(input_bam, ".bam") | ||
| input { | ||
| File input_bam |
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If we call RevertSam through GATK we can use NIO here too, right?
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That's true, but by the time we subset down to just the mt bam everything is pretty quick. The NIO above helps because it's still on the full size hg38 wgs bam.
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Thanks for the review @ldgauthier! Mutect should be up to date (or at least as up to date as we've ever run on our truth sets). I'm going to rebase and hope that tests will pass 🤞 |
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Adds NIO to the SubsetBam task and converts all the MT pipeline WDLs to WDL 1.0. I ran this on one sample in Terra and it worked.